Macromolecule Content

Total Structure Weight: 37.64 kDa
Atom Count: 2,748
Modelled Residue Count: 305
Deposited Residue Count: 318
Unique protein chains: 1

1VHN

Crystal structure of a putative flavin oxidoreductase with flavin

PDB DOI: 10.2210/pdb1VHN/pdb

Classification: Structural genomics, unknown function
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-12-01 Released: 2003-12-30
Deposition Author(s): Structural GenomiX

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.227
R-Value Work: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima.

Park, F., Gajiwala, K., Noland, B., Wu, L., He, D., Molinari, J., Loomis, K., Pagarigan, B., Kearins, P., Christopher, J., Peat, T., Badger, J., Hendle, J., Lin, J., Buchanan, S.

(2004) Proteins 55: 772-774

PubMed: 15103641 Search on PubMed
DOI: 10.1002/prot.20086
Primary Citation of Related Structures:
1VHN

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative flavin oxidoreductase	A	318	Thermotoga maritima	Mutation(s): 7 Gene Names: yacF EC: 1.3.1
UniProt
Find proteins for Q9WXV1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXV1 Go to UniProtKB: Q9WXV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WXV1
Protein Feature View 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 E [auth A] MOL2 format, chain E [auth A]	E [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.227
R-Value Work: 0.189
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.279	α = 90
b = 96.442	β = 90
c = 93.139	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
REFMAC	refinement
CCP4	data scaling
TRUNCATE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-12-30

Deposition Author(s):

Structural GenomiX

Revision History (Full details and data files)

Version 1.0: 2003-12-30
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: 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.