2D5M

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

PDB DOI: https://doi.org/10.2210/pdb2D5M/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-11-02 Released: 2006-11-21
Deposition Author(s): Ueda, Y., Shibata, N., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.162
R-Value Work: 0.128
R-Value Observed: 0.135

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

Ueda, Y., Shibata, N., Higuchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 21.69 kDa
Atom Count: 1,744
Modelled Residue Count: 183
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
flavoredoxin	A	190	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0
UniProt
Find proteins for Q4W5X6 (Desulfovibrio vulgaris) Explore Q4W5X6 Go to UniProtKB: Q4W5X6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4W5X6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.162
R-Value Work: 0.128
R-Value Observed: 0.135
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.346	α = 90
b = 53.346	β = 90
c = 116.224	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-11-21

Deposition Author(s):

Ueda, Y.

Shibata, N.

Higuchi, Y.

Revision History (Full details and data files)

Version 1.0: 2006-11-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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2D5M

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

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)