7JQI | pdb_00007jqi

Structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with alpha-ketoglutarate and NADP+

PDB DOI: https://doi.org/10.2210/pdb7JQI/pdb

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

Deposited: 2020-08-11 Released: 2021-09-08
Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.197 (Depositor), 0.196 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with alpha-ketoglutarate and NADP+

Vuksanovic, N., Silvaggi, N.R.

To be published.

Macromolecule Content

Total Structure Weight: 37.93 kDa
Atom Count: 2,747
Modeled Residue Count: 312
Deposited Residue Count: 325
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate/hydroxypyruvate reductase A	A	325	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)

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.197 (Depositor), 0.196 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.887	α = 90
b = 158.887	β = 90
c = 96.091	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-08
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.