2E83

T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

PDB DOI: https://doi.org/10.2210/pdb2E83/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-01-17 Released: 2008-01-15
Deposition Author(s): Shibata, N., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.188
R-Value Work: 0.161
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of T31V mutant of FMN-binding protein from Desulfovibrio vulgaris Miyazaki F

Shibata, N., Kitamura, M., Higuchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 27.21 kDa
Atom Count: 2,307
Modelled Residue Count: 244
Deposited Residue Count: 244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A, B	122	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 1
UniProt
Find proteins for Q46604 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore Q46604 Go to UniProtKB: Q46604
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46604
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-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: 1.52 Å
R-Value Free: 0.188
R-Value Work: 0.161
R-Value Observed: 0.161
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.615	α = 90
b = 84.394	β = 93.33
c = 40.387	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-01-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.