3HD0 | pdb_00003hd0

Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima

• PDB DOI: https://doi.org/10.2210/pdb3HD0/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-05-06 Released: 2009-07-14 
• Deposition Author(s): Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima

Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82 kDa 
• Atom Count: 5,512 
• Modeled Residue Count: 659 
• Deposited Residue Count: 711 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease V	A, B, C [auth D]	237	Thermotoga maritima	Mutation(s): 0  Gene Names: nfi, TM_1865 EC: 3.1.21.7
UniProt
Find proteins for Q9X2H9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X2H9  Go to UniProtKB:  Q9X2H9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.571	α = 90
b = 71.966	β = 90
c = 120.266	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary