2YYT | pdb_00002yyt

Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus

PDB DOI: https://doi.org/10.2210/pdb2YYT/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.289 (Depositor), 0.294 (DCC)
R-Value Work:
0.229 (Depositor), 0.235 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YYT

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 107.93 kDa
Atom Count: 7,022
Modeled Residue Count: 860
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5L0U0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.289 (Depositor), 0.294 (DCC)
R-Value Work: 0.229 (Depositor), 0.235 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.213	α = 100.74
b = 58.86	β = 96.56
c = 88.135	γ = 107.44

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.