2GR3 | pdb_00002gr3

Crystal structure of Ferredoxin reductase, BphA4 (oxidized form)

PDB DOI: https://doi.org/10.2210/pdb2GR3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas sp. KKS102
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-22 Released: 2007-05-22
Deposition Author(s): Senda, T., Senda, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.190 (Depositor), 0.188 (DCC)
R-Value Observed:
0.191 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A ferredoxin reductase BphA4 uses a butterfly motion of FAD to regulate affinity for ferredoxin

Senda, M., Kishigami, S., Kimura, S., Ishida, T., Fukuda, M., Senda, T.

To be published.

Macromolecule Content

Total Structure Weight: 44.11 kDa
Atom Count: 3,344
Modeled Residue Count: 402
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ferredoxin reductase	A	408	Pseudomonas sp. KKS102	Mutation(s): 1 EC: 1.18.1.2
UniProt
Find proteins for Q52437 (Pseudomonas sp. (strain KKS102)) Explore Q52437 Go to UniProtKB: Q52437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.206 (Depositor), 0.205 (DCC)
R-Value Work: 0.190 (Depositor), 0.188 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.107	α = 90
b = 98.107	β = 90
c = 170.73	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data scaling
XTALVIEW	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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.