2CW8 | pdb_00002cw8

Crystal structure of intein homing endonuclease II

• PDB DOI: https://doi.org/10.2210/pdb2CW8/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-06-17 Released: 2006-04-18 
• Deposition Author(s): Matsumura, H., Takahashi, H., Inoue, T., Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1

Matsumura, H., Takahashi, H., Inoue, T., Yamamoto, T., Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

(2006) Proteins 63: 711-715

• PubMed: 16493661 
• DOI: https://doi.org/10.1002/prot.20858
• Primary Citation Related Structures: 
  2CW7, 2CW8

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Organizational Affiliation: 
• Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.84 kDa 
• Atom Count: 4,735 
• Modeled Residue Count: 537 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease PI-PkoII	A	537	Thermococcus kodakarensis KOD1	Mutation(s): 9  EC: 3.1 (PDB Primary Data), 2.7.7.7 (UniProt)
UniProt
Find proteins for P77933 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore P77933  Go to UniProtKB:  P77933

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.97	α = 90
b = 150.54	β = 90
c = 145.49	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Matsumura, H., Takahashi, H., Inoue, T., Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary