7JQJ | pdb_00007jqj

Structure of W45F Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with NADP+

PDB DOI: https://doi.org/10.2210/pdb7JQJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of W45F Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with NADP+

Vuksanovic, N., Silvaggi, N.R.

To be published.

Macromolecule Content

Total Structure Weight: 37.74 kDa
Atom Count: 2,704
Modeled Residue Count: 310
Deposited Residue Count: 325
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate/hydroxypyruvate reductase A	A	325	Escherichia coli BL21(DE3)	Mutation(s): 1 Gene Names: ghrA, ECBD_2566 EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP 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]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.177	α = 90
b = 159.177	β = 90
c = 95.709	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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Ligand Structure Quality Assessment

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

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.