2PG0 | pdb_00002pg0

Crystal structure of acyl-CoA dehydrogenase from Geobacillus kaustophilus

PDB DOI: https://doi.org/10.2210/pdb2PG0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacillus kaustophilus HTA426
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-06 Released: 2007-05-08
Deposition Author(s): Chen, L., Chen, L.-Q., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Li, Y., Fu, Z.-Q., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of acyl-CoA dehydrogenase from G. kaustophilus

Chen, L., Chen, L.-Q., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Li, Y., Fu, Z.-Q., Rose, J.P., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 88.75 kDa
Atom Count: 6,704
Modeled Residue Count: 757
Deposited Residue Count: 770
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase	A, B	385	Geobacillus kaustophilus HTA426	Mutation(s): 0 Gene Names: GK1316 EC: 1.3.99.3
UniProt
Find proteins for Q5L0D5 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L0D5 Go to UniProtKB: Q5L0D5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5L0D5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-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: 1.80 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.276	α = 90
b = 119.276	β = 90
c = 124.452	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-08

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-05-08
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-09-13
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references, Derived calculations