4W8K | pdb_00004w8k

Crystal structure of a putative Cas1 enzyme from Vibrio phage ICP1

• PDB DOI: https://doi.org/10.2210/pdb4W8K/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vibrio phage ICP1_2005_A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-25 Released: 2014-09-17 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Onopriyeno, O., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

To be published

Savchenko, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.47 kDa 
• Atom Count: 5,016 
• Modeled Residue Count: 586 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas1 protein	A, B	323	Vibrio phage ICP1_2005_A	Mutation(s): 0  Gene Names: TUST1-15_00465
UniProt
Find proteins for A0ACD6B8J2 (Vibrio phage ICP1_2005_A) Explore A0ACD6B8J2  Go to UniProtKB:  A0ACD6B8J2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34w8k

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.59	α = 90
b = 83.32	β = 90
c = 133.98	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Onopriyeno, O., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description