8WTH | pdb_00008wth

Crystal structure of Cas3-HD

PDB DOI: https://doi.org/10.2210/pdb8WTH/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-18 Released: 2024-07-24
Deposition Author(s): Mo, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.295 (Depositor), 0.293 (DCC)
R-Value Work:
0.261 (Depositor), 0.259 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structural insight into dynamic characteristic of the polymerized forms of kinetoplastid membrane protein-11

Mo, X.

To be published.

Macromolecule Content

Total Structure Weight: 22.24 kDa
Atom Count: 1,535
Modeled Residue Count: 186
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD Cas3-type domain-containing protein	A	189	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH0916
UniProt
Find proteins for O58617 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58617 Go to UniProtKB: O58617
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58617
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.295 (Depositor), 0.293 (DCC)
R-Value Work: 0.261 (Depositor), 0.259 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.656	α = 90
b = 41.706	β = 98.881
c = 47.983	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071476

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release
Version 1.1: 2024-10-16
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.