6OVL | pdb_00006ovl

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

• PDB DOI: https://doi.org/10.2210/pdb6OVL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-08 Released: 2020-05-13 
• 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: 2.10 Å
• R-Value Free: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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)

Macromolecule Content 

• Total Structure Weight: 37.35 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 313 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate/hydroxypyruvate reductase A	A	318	Escherichia coli	Mutation(s): 0  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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
PO4	C [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLV	E [auth A]	GLYOXYLIC ACID C2 H2 O3 HHLFWLYXYJOTON-UHFFFAOYSA-N
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.82	α = 90
b = 158.82	β = 90
c = 96.71	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
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: 2020-05-13
  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