Gromacs/C2/PDB-File-Format-and-Website/English - Revision history

Ranipv076 at 13:18, 21 October 2021

2021-10-21T13:18:33Z

Ranipv076 at 13:11, 21 October 2021

2021-10-21T13:11:40Z

Ranipv076 at 13:07, 21 October 2021

2021-10-21T13:07:57Z

Ranipv076 at 13:03, 21 October 2021

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Ranipv076 at 13:01, 21 October 2021

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Snehalathak at 12:36, 21 October 2021

2021-10-21T12:36:48Z

Ranipv076: Created page with " {| border =1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the tutorial on '''PDB File Format and Website'''. |- || ''..."

2021-09-21T14:55:38Z

Created page with " {| border =1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the tutorial on '''PDB File Format and Website'''. |- || ''..."

New page

{| border =1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''PDB File Format and Website'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn,

* About PDB file format for molecular structure
* Protein Data Bank ('''PDB''') website
* Download a '''pdb''' file from '''PDB''' website
* About '''FASTA''' file format

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36.2
* A working internet connection to access the '''PDB''' website

|-
|| '''Slide Number 4'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''File from downloaded tarball'''
|| Files used in this tutorial, can be found in the,
* Downloaded and extracted tarball directory used for '''Gromacs''' installation

|-
|| Open the File manager.
|| Let’s open the '''File manager'''.

Go to the downloaded and extracted tarball directory for '''Gromacs''' installation.

|-
|| Cursor on the files of the extracted '''Gromacs''' directory.

Go to '''src''' directory.
|| Few test '''PDB''' files are given for testing purposes with '''Gromacs''' installation.

They can be found in the '''src''' directory of the extracted tarball of '''Gromacs'''.

|-
|| Navigate to '''testutils''' directory and then to '''simulationdatabase'''.
|| Now, navigate to '''testutils''' directory and then to '''simulationdatabase'''.

|-
|| Scroll down and cursor on the '''lysozyme.pdf''' file.
|| Scroll down and notice the '''lysozyme.pdb''' file.

|-
|| Open '''lysozyme.pdb''' in a text editor.
|| Let’s open this file in a text editor.

This file is in '''PDB '''file format, and the structure of truncated '''lysozyme'''.

|-
|| Cursor on the file.
|| The file gives the coordinates in '''xyz''' axes of each atom in a molecule.

It is in the '''PDB''' format defined by '''IUPAC''' convention.

|-
|| '''Slide Number 6'''

'''Protein Data Bank'''
[https://www.rcsb.org/ https://www.rcsb.org/] '''
|| * '''Protein data bank''' is a repository of 3D structural data of biomolecules
* The website is shown here.
* The structures are determined by '''X-ray''' diffraction, '''NMR''', '''electron microscopy'''

|-
|| '''Slide Number 7'''

'''Protein Data Bank'''
|| Atomic resolution structures for
* Proteins, DNA and RNA
* Carbohydrates and lipids
* Several ligand molecules
are available here

|-
|| Cursor on the first 3 lines.
|| The first few lines on the top are comments, giving details about the file.

|-
|| Cursor on '''MODEL'''.
|| The '''MODEL''' indicates the first set of coordinates are listed below it.

This happens when more than a single coordinate set is selected to represent the molecule.

|-
|| Cursor on page.
|| Learner can refer to structures determined by NMR method, to know more.

An ensemble of structure is selected to represent the molecule.

|-
|| Cursor on the '''ATOM''' lines.
|| Notice the several columns below '''MODEL'''.

Each row gives details of each '''atom''' in the biomolecule.

|-
|| Cursor on the first and second column.
|| The first column shows, it is for the atom.

The second column incrementally counts each atom in the molecule.

|-
|| Cursor on the third and fourth column.
|| Third column gives the atom name.

Fourth column shows the atom is in a '''Lysine''' residue.

|-
|| Cursor on 5th and 6th column.
|| Fifth column is the subunit number.

Sixth column is the residue position number of the atom in the biomolecule.

|-
|| Cursor on 7, 8, and 9 columns.
|| The next three columns are the '''x, y''', and '''z''' coordinates.

They are the position of the atom in the biomolecule in 3 dimensional space.

|-
|| Cursor on the 10th column.
|| The 10th column is the occupancy of the atom at that position.

|-
|| Cursor on 11th and 12th column.
|| Then notice the '''R''' factor.

The last column lists the element that occupies the position.

|-
|| Scroll down and show '''TER''' line in the file.
|| Scroll to the end of the file and notice the TER.

This denotes the end of the molecular model and the molecule.

|-
|| Cursor on residue number 10.
|| Notice that the data is truncated at the 10th residue in this document.

This file is for demonstration purpose only.

|-
|| Cursor on the interface and close the text editor.
|| All the residues for '''1AKI''' are not present here.

Lysozyme, or full length deposition of '''1AKI''' has 129 amino acid residues.

Let’s consult the '''PDB''' site to know more.

Let’s close the text editor file.

|-
|| Open web browser and go to [https://www.rcsb.org/ https://www.rcsb.org/] .
|| Next, open a web browser.

Go to the '''PDB''' website as seen here.

Let’s learn to search and download coordinates from the '''PDB''' website.

|-
|| Enter '''lysozyme''' in the search form on top and press '''Enter'''.
|| In the search form on the top, let’s enter '''lysozyme'''.

|-
|| Scroll down.
|| Scroll down the page and notice the several search results for '''lysozyme'''.

Each molecular structure that is deposited in the '''PDB''' has a unique ID.

|-
|| Scroll up and enter '''1AKI''' in the search form.
|| Now, go to the top of the page.

Click on '''Search, Basic Search'''.

Let’s search for the structure deposition ID '''1AKI'''.

|-
|| Show details of '''1AKI'''.
|| Now the structure deposition details of this protein ID, appears.
The page opens in the '''structure summary''' tab.

|-
|| Cursor on the page and scroll down.
|| Scroll down and notice the detailed information on this structure.

It is that of egg white '''lysozyme'''.

|-
|| Cursor on '''X-ray diffraction'''.
|| Notice that it is determined by '''X-ray diffraction''' method.

|-
|| Click on '''3D View''' tab.
Scroll down the page.
|| Scroll to the top of the page and click on the '''3D View''' tab.

Scroll down the page.

An interactive window on the left with the protein structure.

|-
|| Click, hold and move mouse, show protein in rotated view.
|| Click, hold and move the mouse to rotate the protein in the window.

|-
|| Cursor on primary sequence and click on 2-3 residues.

Move cursor to the protein to show the highlighted position.
|| On the top of the screen, notice the protein primary sequence.

Click on any of the residue and notice it highlighted in the structure.

|-
|| Cursor on the protein structure.
|| Currently, the secondary structure of the protein is also visible.

|-
|| Cursor on red dot.
|| All the red dots are water molecules.

Users may pause this video and explore all the details given on this '''PDB''' ID.

|-
|| Scroll up the page.
|| Let’s scroll up the page and download the molecule structure coordinate file.

|-
|| Cursor on '''Display files''' and '''Download files'''.
|| Notice the '''Display files''' and '''Download files''' pulldown towards the top right.

|-
|| Click on the '''Display files'''.
|| Click on the '''Display files''' and notice the '''FASTA''' '''Sequence''' option.

|-
|| Click on '''FASTA'''.
|| Click on it.

|-
|| Cursor on the '''FASTA''' sequence tab.
|| A new tab opens with the '''primary''' sequence of the protein in single letter code.

The first line is the header giving the ID and details about the sequence.

|-
|| Close the '''FASTA''' tab.
|| I will close this tab.

|-
|| Click on the '''PDB format''' option.
|| Next click on the '''PDB format''' option in the '''Display files''' pulldown.

|-
|| Cursor on the new tab with the '''PDB''' file.
|| Again, a new tab opens with the '''PDB''' file.

|-
|| Cursor on the header lines.
|| The first several lines are headers which give details about the deposition.

|-
|| Cursor on details on top.
|| Notice the organism, name, authors, publication details and resolution.

|-
|| Scroll down the page.
|| Scroll down the page and notice more details.

Learner may pause this video and explore the PDB file in detail.

|-
|| Cursor on '''SSBOND'''.
|| Any disulfide bond present in the protein is also listed here.

|-
||
|| Often small molecule ligand or more chains are present in the system of study.

If so, their details will also be visible in the header.

|-
|| Cursor on the atomic coordinates.
|| The coordinates for each atom in the unit structure is listed below.

|-
|| Cursor on the atomic coordinates.
|| Notice that there are no hydrogens listed here.

This is because the x-ray diffraction method does not detect hydrogens.

|-
|| Screenshot of '''1AKI''' file opened in text editor.
|| The '''1AKI''' file, which we opened earlier, had hydrogen atoms added to the file.

That file also has a trimmed header.

Hydrogen atoms are added to the molecule afterwards as needed by the users.

|-
|| Scroll down.

Cursor at '''TER'''.
|| Now, scroll almost to the end of the page.

|-
|| Cursor on '''HETATM'''.

Point to the HOH atoms in the file.
|| Below '''TER''' tag, this there are many hetero atoms listed now.

They are water molecules that are present in the protein crystal.

|-
|| Show '''O''' element for '''HETATM'''.
|| Notice that, here too, hydrogens will not be observed.

|-
|| Show '''O''' element for '''HETATM'''.
|| Often, these water molecules are removed from the PDB file, before simulation.

|-
|| Close the '''PDB''' details tab.
|| Let’s close the '''PDB''' details tab.

|-
|| Click on the '''Download Files''' pulldown.
|| Now, click on the '''Download Files''' pulldown.

|-
|| Choose the '''PDB format'''.
|| Choose the '''PDB format'''.

A dialog box may or may not open prompting to save the file.

|-
|| Choose '''Save File''' and click on '''Ok'''.
|| If so, choose to save the file on the computer and click on '''Ok'''.

Allow the file download to complete.

|-
|| Cursor on the PDB web page.
|| Learner may pause this video and open the downloaded file in a text editor.

Notice that the file we viewed and downloaded are the same.

|-
|| Cursor on the PDB web page.
|| Open the '''PDB''' file in '''VMD''' or another molecular viewer.

Notice the structure displayed.

|-
|| '''Slide Number 8'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* The '''PDB''' file format
* The '''PDB''' website
* '''FASTA''' file format
* Header details in '''PDB''' file
* Downloaded a '''pdb''' file

|-
|| '''Slide Number 9'''

'''Assignment '''
|| For assignment activity, please do the following.

* Go through the '''PDB''' website
* Familiarize with more details given for the PDB deposition.
* Go through the header details of the file that is downloaded.

|-
|| '''Slide Number 10'''

'''Assignment '''
|| Go through the given IDs from '''PDB''' website for enzyme '''DHFR''' and it’s complexes.

* '''2L28''' for '''apo enzyme''' and multiple '''conformer'''s
* '''1DIS''' for '''binary''' complex
* '''3DAT''' for '''ternary''' complex

|-
|| '''Slide Number 11'''

'''Assignment '''
||
* Notice the presence and absence of hydrogen atoms in the structure files
* Familiarize with
** Conformational changes in the enzyme
** Hydrogen bonding with ligands

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''

|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

@@ Line 322: / Line 322: @@
 |-
-|| Screenshot of '''1AKI''' file opened in text editor.
+|| Curson on '''1AKI''' file opened in text editor.
 || The '''1AKI''' file, which we opened earlier, had hydrogen atoms added to the file.
-That file also has a trimmed header.
+The file also had a trimmed header.
 Hydrogen atoms are added to the molecule afterwards as needed by the users.
@@ Line 392: / Line 392: @@
 * The '''PDB''' website
 * '''FASTA''' file format
-* Header details in '''PDB''' file
+* Header details in the '''PDB''' file
 * Downloaded a '''pdb''' file

@@ Line 167: / Line 167: @@
 |-
 || Cursor on residue number 10.
-|| Notice that the data is truncated at the 10th residue in this document.
+|| Notice that, the data is truncated at the 10th residue in this document.
 This file is for demonstration purpose only.
@@ Line 173: / Line 173: @@
 |-
 || Cursor on the interface and close the text editor.
-|| All the residues for '''1AKI''' are not present here.
+|| All residues for '''1AKI''' which is the '''lysozyme''' entry are not present here.
 Lysozyme, or full length deposition of '''1AKI''' has 129 amino acid residues.
@@ Line 179: / Line 179: @@
 Let’s consult the '''PDB''' site to know more.
-Let’s close the text editor file.
+Let’s close the text editor.
 |-
@@ Line 210: / Line 210: @@
 || Show details of '''1AKI'''.
 || Now the structure deposition details of this protein ID, appears.
-The page opens in the '''structure summary''' tab.
+The page opens in the '''Structure Summary''' tab.
 |-
@@ Line 224: / Line 224: @@
 |-
 || Click on '''3D View''' tab.
-Scroll down the page.
+Scroll to the top of the page.
 || Scroll to the top of the page and click on the '''3D View''' tab.
 Scroll down the page.
-An interactive window on the left with the protein structure.
+An interactive window is seen on the left with the protein structure.
 |-

@@ Line 109: / Line 109: @@
 |-
 || Cursor on '''MODEL'''.
-|| The '''MODEL''' indicates the first set of coordinates are listed below it.
+|| The '''MODEL''' indicates the first set of coordinates which is listed below it.
 This happens when more than a single coordinate set is selected to represent the molecule.
@@ Line 115: / Line 115: @@
 |-
 || Cursor on page.
-|| Learner can refer to structures determined by NMR method, to know more.
+|| Learner can refer to structures determined by '''NMR''' method, to know more.
-An ensemble of structure is selected to represent the molecule.
+In '''NMR''' an ensemble of structure is selected to represent the molecule.
 |-
@@ Line 135: / Line 135: @@
 || Third column gives the atom name.
-Fourth column shows the atom is in a '''Lysine''' residue.
+The next column shows the amino acid residue.
 |-
@@ Line 161: / Line 161: @@
 |-
 || Scroll down and show '''TER''' line in the file.
-|| Scroll to the end of the file and notice the TER.
+|| Scroll to the end of the file and notice the '''TER''' written here.
 This denotes the end of the molecular model and the molecule.

@@ Line 87: / Line 87: @@
 '''Protein Data Bank'''
 [https://www.rcsb.org/ https://www.rcsb.org/] '''
 || * '''Protein data bank''' is a repository of 3D structural data of biomolecules
 * The website link is shown here.
-* The structures are determined by '''X-ray''' diffraction, '''NMR''', '''electron microscopy'''
+* The structures are determined by '''X-ray''' diffraction, '''NMR''', & '''electron microscopy'''
 |-

@@ Line 36: / Line 36: @@
 '''Pre-requisites'''
 [https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
 || To follow this tutorial,