2CZE | pdb_00002cze

Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with UMP

• PDB DOI: https://doi.org/10.2210/pdb2CZE/pdb

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


• Deposited: 2005-07-13 Released: 2006-01-13 
• Deposition Author(s): Arai, R., Ito, K., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with UMP

Arai, R., Ito, K., Kishishita, S., Shirouzu, M., Yokoyama, S.

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: 46.38 kDa 
• Atom Count: 3,580 
• Modeled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	208	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: pyrF, PH0731 EC: 4.1.1.23
UniProt
Find proteins for O58462 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58462  Go to UniProtKB:  O58462

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], F [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.029	α = 90
b = 85.512	β = 105.71
c = 63.935	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-13 
Deposition Author(s): Arai, R., Ito, K., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description