3AMF

E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

PDB DOI: https://doi.org/10.2210/pdb3AMF/pdb

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

Deposited: 2010-08-19 Released: 2011-10-05
Deposition Author(s): Sato, S., Nakanishi, T., Inoue, H., Kitamura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.224
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Sato, S., Nakanishi, T., Inoue, H., Kitamura, M.

To be published.

Macromolecule Content

Total Structure Weight: 27.35 kDa
Atom Count: 2,196
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 Gene Names: DvMF_2023
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 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 E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.224
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.129	α = 90
b = 60.443	β = 90
c = 72.002	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3AMF

E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Crystal structure of E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)