2YX5 | pdb_00002yx5

Crystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway

PDB DOI: https://doi.org/10.2210/pdb2YX5/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-24 Released: 2007-10-30
Deposition Author(s): Kanagawa, M., Baba, S., Agari, Y., Chen, L.Q., Fu, Z.-Q., Chrzas, J., Wang, B.C., 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:
0.284 (Depositor), 0.283 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway

Kanagawa, M., Baba, S., Agari, Y., Chen, L.Q., Fu, Z.-Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

To be published.

Macromolecule Content

Total Structure Weight: 9.71 kDa
Atom Count: 685
Modeled Residue Count: 82
Deposited Residue Count: 83
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0062 protein MJ1593	A	83	Methanocaldococcus jannaschii	Mutation(s): 0 EC: 6.3.5.3
UniProt
Find proteins for Q58988 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58988 Go to UniProtKB: Q58988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58988
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.284 (Depositor), 0.283 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.251	α = 90
b = 96.251	β = 90
c = 48.257	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-30

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Refinement description

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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.