2ZV3 | pdb_00002zv3

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

PDB DOI: https://doi.org/10.2210/pdb2ZV3/pdb

Classification: HYDROLASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Mutation(s): No

Deposited: 2008-10-31 Released: 2009-05-05
Deposition Author(s): Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.263 (Depositor), 0.261 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

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

Literature

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

Shimizu, K., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 114.24 kDa
Atom Count: 8,466
Modeled Residue Count: 1,005
Deposited Residue Count: 1,035
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H, I	115	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 EC: 3.1.1.29
UniProt
Find proteins for Q60363 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60363 Go to UniProtKB: Q60363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60363
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.263 (Depositor), 0.261 (DCC)
R-Value Work: 0.218 (Depositor), 0.217 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.85	α = 90
b = 70.79	β = 121.67
c = 96.01	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2009-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
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.