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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: in silico

Literature

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

Mo, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.260 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Mo, X.

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

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary