5UTM | pdb_00005utm

Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

PDB DOI: https://doi.org/10.2210/pdb5UTM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus agalactiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-02-15 Released: 2018-02-28
Deposition Author(s): Schormann, N., Ulett, G.C., Chattopadhyay, D.
Funding Organization(s): Australian Res. Council (AU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.220 (Depositor), 0.229 (DCC)
R-Value Work:
0.196 (Depositor), 0.205 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Mutant Structures of Streptococcus agalactiae GAPDH

Schormann, N., Ulett, G.C., Chattopadhyay, D.

To be published.

Macromolecule Content

Total Structure Weight: 155.5 kDa
Atom Count: 11,147
Modeled Residue Count: 1,345
Deposited Residue Count: 1,424
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	356	Streptococcus agalactiae	Mutation(s): 1 Gene Names: gapA, gap, AMR84_09125, AX245_09885, BBP08_10800, DX05_09270, EN72_09590, ERS039640_00200, RDF_1710, TH70_1537 EC: 1.2.1
UniProt
Find proteins for Q9ALW2 (Streptococcus agalactiae) Explore Q9ALW2 Go to UniProtKB: Q9ALW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ALW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.220 (Depositor), 0.229 (DCC)
R-Value Work: 0.196 (Depositor), 0.205 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.991	α = 90
b = 108.258	β = 106.05
c = 90.649	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Schormann, N.

Ulett, G.C.

Chattopadhyay, D.

Funding Organization	Location	Grant Number
Australian Res. Council (AU)	Australia	FT110101048

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description

5UTM | pdb_00005utm

Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Literature

Mutant Structures of Streptococcus agalactiae GAPDH

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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