6UTO | pdb_00006uto

Native E. coli Glyceraldehyde 3-phosphate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb6UTO/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 72.66 kDa 
• Atom Count: 5,825 
• Modelled Residue Count: 660 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3P (Subject of Investigation/LOI)	F [auth A], H [auth B]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	C, D	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.273	α = 90
b = 186.709	β = 90
c = 122.132	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-09
  Changes: Advisory, Data collection, Database references, Structure summary