6P35

2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with 2-keto arginine and NADP

• PDB DOI: https://doi.org/10.2210/pdb6P35/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-22 Released: 2020-05-27 
• Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP

Vuksanovic, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.92 kDa 
• Atom Count: 2,718 
• Modelled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate/hydroxypyruvate reductase A	A	312	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: ghrA, ECBD_2566 EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
UniProt
Find proteins for P75913 (Escherichia coli (strain K12)) Explore P75913  Go to UniProtKB:  P75913

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	F [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
NWG (Subject of Investigation/LOI)	B [auth A], E [auth A]	5-[(diaminomethylidene)amino]-2-oxopentanoic acid C6 H11 N3 O3 ARBHXJXXVVHMET-UHFFFAOYSA-N
SO4	G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.578	α = 90
b = 158.578	β = 90
c = 98.285	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Currently 6P35 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description