5O0V | pdb_00005o0v

crystal structure of E. coli GAP-DH by fortuitous crystallization as an impurity from a solution of human liver FBPase

• PDB DOI: https://doi.org/10.2210/pdb5O0V/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-17 Released: 2017-07-12 
• Deposition Author(s): Ruf, A., Benz, J., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

fortuitous crystallization of GAP-DH impurity from a solution of human liver FBPase

Ruf, A., Benz, J., Rudolph, M.G.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 35.63 kDa 
• Atom Count: 2,640 
• Modeled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase A	A	330	Escherichia coli	Mutation(s): 0  Gene Names: gapA, b1779, JW1768 EC: 1.2.1.12
UniProt
Find proteins for P0A9B2 (Escherichia coli (strain K12)) Explore P0A9B2  Go to UniProtKB:  P0A9B2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.384	α = 90
b = 121.384	β = 90
c = 157.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SADABS	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Ruf, A., Benz, J., Rudolph, M.G.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 2.0: 2017-07-19
  Changes: Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2018-05-23
  Changes: Data collection, Database references, Source and taxonomy
• Version 2.2: 2024-05-08
  Changes: Data collection, Database references