6P35 | pdb_00006p35

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.206 (Depositor), 0.204 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NWG (Subject of Investigation/LOI) Query on NWG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A]	B [auth A], E [auth A]	5-[(diaminomethylidene)amino]-2-oxopentanoic acid C₆ H₁₁ N₃ O₃ ARBHXJXXVVHMET-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.206 (Depositor), 0.204 (DCC)
R-Value Work: 0.171 (Depositor), 0.173 (DCC)
R-Value Observed: 0.173 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Vuksanovic, N.

Silvaggi, N.R.

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

Revision History (Full details and data files)

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
Version 1.3: 2024-10-16
Changes: Structure summary