2IT3 | pdb_00002it3

Structure of PH1069 protein from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb2IT3/pdb

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

Deposited: 2006-10-18 Released: 2007-11-13
Deposition Author(s): Lokanath, N.K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.270 (Depositor), 0.274 (DCC)
R-Value Work:
0.240 (Depositor), 0.237 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Structure of PH1069 protein from Pyrococcus horikoshii

Lokanath, N.K., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 47.09 kDa
Atom Count: 3,434
Modeled Residue Count: 391
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0130 protein PH1069	A, B	200	Pyrococcus horikoshii	Mutation(s): 0 EC: 2.1.1.282
UniProt
Find proteins for O58796 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58796 Go to UniProtKB: O58796
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58796
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.270 (Depositor), 0.274 (DCC)
R-Value Work: 0.240 (Depositor), 0.237 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.673	α = 90
b = 57.951	β = 90
c = 167.416	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-10-30
Changes: Structure summary

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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.