2DYY

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb2DYY/pdb

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

Deposited: 2006-09-19 Released: 2007-03-19
Deposition Author(s): Ihsanawati, Kishishita, S., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.295
R-Value Work: 0.209
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

Ihsanawati, Kishishita, S., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Bessho, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 168.63 kDa
Atom Count: 11,461
Modelled Residue Count: 1,456
Deposited Residue Count: 1,512
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0076 protein PH0854	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	126	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O58584 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58584 Go to UniProtKB: O58584
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58584
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.295
R-Value Work: 0.209
R-Value Observed: 0.209
Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.49	α = 90
b = 43.09	β = 91.51
c = 170.21	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-19

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-03-19
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Refinement description

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.