1VHN | pdb_00001vhn

Crystal structure of a putative flavin oxidoreductase with flavin

• PDB DOI: https://doi.org/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.227 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.180 (DCC) 

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 
• DOI: https://doi.org/10.1002/prot.20086
• Primary Citation of Related Structures:  
  1VHN

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Organizational Affiliation: 
• Structural GenomiX, Inc., San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.180 (DCC) 

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

Entry History 

Deposition Data

• Released Date: 2003-12-30 
Deposition Author(s): Structural GenomiX

Revision History  

• 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
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary