3GR7

Structure of OYE from Geobacillus kaustophilus, hexagonal crystal form

PDB DOI: https://doi.org/10.2210/pdb3GR7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacillus kaustophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-25 Released: 2010-03-31
Deposition Author(s): Uhl, M.K., Gruber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.223
R-Value Work: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones

Schittmayer, M., Zach, S., Winkler, M., Winkler, A., Macheroux, P., Uhl, M.K., Gruber, K., Kambourakis, S., Rozzell, D., Glieder, A.

(2011) Adv Synth Catal 353: 268-274

DOI: https://doi.org/10.1002/adsc.201000862

Macromolecule Content

Total Structure Weight: 76.75 kDa
Atom Count: 5,790
Modelled Residue Count: 680
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase	A, B	340	Geobacillus kaustophilus	Mutation(s): 0 Gene Names: namA EC: 1.6.99.1
UniProt
Find proteins for Q5KXG9 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KXG9 Go to UniProtKB: Q5KXG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5KXG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.223
R-Value Work: 0.200
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.99	α = 90
b = 101.99	β = 90
c = 260.97	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Uhl, M.K.

Gruber, K.

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-09-03
Changes: Database references
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3GR7

Structure of OYE from Geobacillus kaustophilus, hexagonal crystal form

Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)