Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.13 kDa 
• Atom Count: 2111 
• Modelled Residue Count: 201 
• Deposited Residue Count: 206 
• Unique protein chains: 1

3OQ2

Structure of a CRISPR associated protein Cas2 from Desulfovibrio vulgaris

• PDB DOI: 10.2210/pdb3OQ2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Desulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-02 Released: 2010-12-22 
• Deposition Author(s): Samai, P., Smith, P., Shuman, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.177 
• R-Value Work: 0.128 
• R-Value Observed: 0.130 

Literature

Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris.

Samai, P., Smith, P., Shuman, S.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1552-1556

• PubMed: 21139194 
• DOI: 10.1107/S1744309110039801
• Primary Citation of Related Structures:  
  3OQ2


• PubMed Abstract: 
  

CRISPRs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with RNA-guided acquired immunity to invasive DNAs. CRISPR-associated (Cas) proteins carry out the immune effector functions. Cas2 is a universal component of the CRISPR system. Here, a 1.35 Å resolution crystal structure of Cas2 from the bacterium Desulfovibrio vulgaris (DvuCas2) is reported. DvuCas2 is a homodimer, with each protomer consisting of an N-terminal βαββαβ ferredoxin fold (amino acids 1-78) to which is appended a C-terminal segment (amino acids 79-102) that includes a short 3(10)-helix and a fifth β-strand. The β5 strands align with the β4 strands of the opposite protomers, resulting in two five-stranded antiparallel β-sheets that form a sandwich at the dimer interface. The DvuCas2 dimer is stabilized by a distinctive network of hydrophilic cross-protomer side-chain interactions.

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Organizational Affiliation: 

Molecular Biology Program, Sloan-Kettering Institute for Cancer Research, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Cas2	A, B	103	Desulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: cas2, DVUA0135 EC: 3.1
UniProt
Find proteins for Q72WF4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72WF4  Go to UniProtKB:  Q72WF4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	I [auth A], K [auth B], L [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	F [auth A], G [auth A], H [auth A], J [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.177 
• R-Value Work: 0.128 
• R-Value Observed: 0.130 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.874	α = 90
b = 48.81	β = 99.2
c = 41.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-02 
• Released Date: 2010-12-22 
Deposition Author(s): Samai, P., Smith, P., Shuman, S.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-09-13
  Changes: Refinement description