2OU5 | pdb_00002ou5

Crystal structure of a pyridoxamine 5'-phosphate oxidase-related fmn-binding protein (jann_0254) from jannaschia sp. ccs1 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OU5/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Jannaschia sp. CCS1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-02-09 Released: 2007-03-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of pyridoxamine 5'-phosphate oxidase-related FMN-binding (YP_508196.1) from Jannaschia sp. CCS1 at 1.60 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.1 kDa 
• Atom Count: 3,268 
• Modeled Residue Count: 350 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase-related, FMN-binding	A, B	175	Jannaschia sp. CCS1	Mutation(s): 2  Gene Names: YP_508196.1, Jann_0254

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OU5

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.88	α = 90
b = 68.51	β = 90
c = 111.92	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary