2YYU | pdb_00002yyu

Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus

• PDB DOI: https://doi.org/10.2210/pdb2YYU/pdb

• Classification: LYASE
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-02 Released: 2007-11-06 
• Deposition Author(s): Kanagawa, M., Baba, S., Nakamura, Y., Bessho, Y., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.272 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus

Kanagawa, M., Baba, S., Nakamura, Y., Bessho, Y., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 54.61 kDa 
• Atom Count: 3,717 
• Modeled Residue Count: 454 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	246	Geobacillus kaustophilus HTA426	Mutation(s): 0  EC: 4.1.1.23
UniProt
Find proteins for Q5L0U0 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L0U0  Go to UniProtKB:  Q5L0U0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5P	C [auth A], D [auth B]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.272 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.65	α = 90
b = 70.151	β = 106.86
c = 62.865	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Kanagawa, M., Baba, S., Nakamura, Y., Bessho, Y., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations