6UTM | pdb_00006utm

Native E. coli Glyceraldehyde 3-phosphate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb6UTM/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-29 Released: 2019-12-11
Deposition Author(s): Rodriguez-Hernandez, A., Romo-Arevalo, E., Rodriguez-Romero, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.199 (Depositor), 0.201 (DCC)
R-Value Work:
0.161 (Depositor), 0.165 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Novel Substrate-Binding Site in the X-Ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

Rodriguez-Hernandez, A., Romo-Arevalo, E., Rodriguez-Romero, A.

(2019) Crystals (Basel) 9: 622

DOI: https://doi.org/10.3390/cryst9120622

Macromolecule Content

Total Structure Weight: 71.49 kDa
Atom Count: 5,373
Modeled Residue Count: 660
Deposited Residue Count: 660
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	330	Escherichia coli	Mutation(s): 0 Gene Names: gapA, ACN002_1253 EC: 1.2.1 (PDB Primary Data), 1.2.1.12 (UniProt)
UniProt
Find proteins for P0A9B2 (Escherichia coli (strain K12)) Explore P0A9B2 Go to UniProtKB: P0A9B2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9B2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G3P (Subject of Investigation/LOI) Query on G3P Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.199 (Depositor), 0.201 (DCC)
R-Value Work: 0.161 (Depositor), 0.165 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.912	α = 90
b = 186.966	β = 90
c = 121.751	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

Rodriguez-Hernandez, A.

Romo-Arevalo, E.

Rodriguez-Romero, A.

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Refinement description

6UTM | pdb_00006utm

Native E. coli Glyceraldehyde 3-phosphate dehydrogenase

Literature

A Novel Substrate-Binding Site in the X-Ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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