4WJ0 | pdb_00004wj0

Structure of PH1245, a cas1 from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb4WJ0/pdb
Entry: 4WJ0 supersedes: 3PV9

Classification: IMMUNE SYSTEM
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-29 Released: 2014-10-15
Deposition Author(s): Petit, P., Brown, G., Savchenko, A., Yakunin, A.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.282 (Depositor), 0.279 (DCC)
R-Value Work:
0.227 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of PH1245, a cas1 from Pyrococcus horikoshii

Petit, P., Brown, G., Savchenko, A., Yakunin, A.F.

To be published.

Macromolecule Content

Total Structure Weight: 75.7 kDa
Atom Count: 5,165
Modeled Residue Count: 624
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas1	A, B	322	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: cas1, PH1245 EC: 3.1
UniProt
Find proteins for O58938 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58938 Go to UniProtKB: O58938
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58938
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.282 (Depositor), 0.279 (DCC)
R-Value Work: 0.227 (Depositor), 0.228 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.89	α = 90
b = 58.672	β = 90
c = 90.147	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

This entry supersedes: 3PV9

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy

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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.