2CW7 | pdb_00002cw7

Crystal structure of intein homing endonuclease II

PDB DOI: https://doi.org/10.2210/pdb2CW7/pdb

Classification: HYDROLASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.243 (Depositor), 0.242 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.

Macromolecule Content

Total Structure Weight: 62.57 kDa
Atom Count: 4,426
Modeled Residue Count: 537
Deposited Residue Count: 537
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease PI-PkoII	A	537	Thermococcus kodakarensis KOD1	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77933
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.243 (Depositor), 0.242 (DCC)
R-Value Work: 0.206 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.7	α = 90
b = 149.06	β = 90
c = 146.13	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-04-18

Deposition Author(s):

Revision History (Full details and data files)

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: 2024-03-13
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description