1FVP | pdb_00001fvp

FLAVOPROTEIN 390

• PDB DOI: https://doi.org/10.2210/pdb1FVP/pdb

• Classification: FLAVIN-BINDING PROTEIN
• Organism(s): Photobacterium phosphoreum
• Mutation(s): No 


• Deposited: 1995-07-07 Released: 1995-10-15 
• Deposition Author(s): Kita, A., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work: 
  0.240 (Depositor) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Structure of flavoprotein FP390 from a luminescent bacterium Photobacterium phosphoreum refined at 2.7 A resolution.

Kita, A., Kasai, S., Miyata, M., Miki, K.

(1996) Acta Crystallogr D Biol Crystallogr 52: 77-86

• PubMed: 15299728 
• DOI: https://doi.org/10.1107/S0907444995009796
• Primary Citation Related Structures: 
  1FVP


• PubMed Abstract: 
  

  The three-dimensional structure of a flavoprotein, FP(390), from a luminescent bacterium, Photobacterium phosphoreum, solved by the molecular-replacement method, was refined to an R factor of 24.0% for 17 433 independent reflections, from 6.0 to 2.7 A resolution, collected by synchrotron radiation. The asymmetric unit of the crystal (space group P4(3)22, a = b = 76.8 and c = 242 A) contains two monomer molecules related by a non-crystallographic twofold axis to form a dimer. There are two Q-flavin [flavin mononucleotide (FMN) with myristic acid] molecules in FP(390) monomer. One of them is located at the interface of dimer which is bound to both monomer and the another is at the molecular surface. The electron density of myristic acids of Q-flavins at the dimer interface in both monomer are weak and unclear, showing the possibility that the Q-flavins bound in this site are not a single species but a mixture of two components, 6-(3"-myristic acid)-FMN and 6-(4"- myristic acid)-FMN.

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Organizational Affiliation: 
• Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.02 kDa 
• Atom Count: 3,997 
• Modeled Residue Count: 462 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAVOPROTEIN 390	A, B	231	Photobacterium phosphoreum	Mutation(s): 0
UniProt
Find proteins for P12745 (Photobacterium phosphoreum) Explore P12745  Go to UniProtKB:  P12745

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMA	C [auth A], D [auth A], E [auth B], F [auth B]	6-(3-TETRADECANOIC ACID) FLAVINE MONONUCLEOTIDE C31 H47 N4 O11 P ZMESPPGIOMLBCU-QPLRPWAESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work:  0.240 (Depositor) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.8	α = 90
b = 76.8	β = 90
c = 242	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
WEIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-10-15 
Deposition Author(s): Kita, A., Miki, K.

Revision History  

• Version 1.0: 1995-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations