2R6V | pdb_00002r6v

Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii at 1.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2R6V/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-06 Released: 2007-09-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.57 kDa 
• Atom Count: 1,893 
• Modelled Residue Count: 182 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein PH0856	A	191	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: NP_142786.1, PH0856
UniProt
Find proteins for O58586 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58586  Go to UniProtKB:  O58586

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
NCA	C [auth A]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.25 Å
• R-Value Free:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32R6V

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.2	α = 90
b = 46.2	β = 90
c = 267.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary