3WBY | pdb_00003wby

Crystal structure of Gox0644 D53A mutant in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb3WBY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gluconobacter oxydans 621H
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-05-22 Released: 2014-05-28
Deposition Author(s): Yuan, Y.A., Wang, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.326 (Depositor), 0.321 (DCC)
R-Value Work:
0.218 (Depositor), 0.216 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3WBY

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Gox0644 D53A mutant in complex with NADPH

Yuan, Y.A., Wang, C.

To be published.

Macromolecule Content

Total Structure Weight: 65.51 kDa
Atom Count: 4,454
Modeled Residue Count: 542
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 2,5-diketo-D-gluconic acid reductase	A, B	282	Gluconobacter oxydans 621H	Mutation(s): 1 Gene Names: GOX0644 EC: 1.1.1
UniProt
Find proteins for Q5FT75 (Gluconobacter oxydans (strain 621H)) Explore Q5FT75 Go to UniProtKB: Q5FT75
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FT75
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.326 (Depositor), 0.321 (DCC)
R-Value Work: 0.218 (Depositor), 0.216 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.638	α = 90
b = 76.587	β = 90
c = 125.624	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.