1J6O | pdb_00001j6o

Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1J6O/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-07-09 Released: 2002-10-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.84 kDa 
• Atom Count: 2,296 
• Modeled Residue Count: 260 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TatD-related deoxyribonuclease	A	268	Thermotoga maritima	Mutation(s): 1  Gene Names: TM0667 EC: 3.1.21
UniProt
Find proteins for Q9WZD5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZD5  Go to UniProtKB:  Q9WZD5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-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: 1.80 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31J6O

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.05	α = 90
b = 77.25	β = 90
c = 84.53	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
CCP4	data reduction
SnB	phasing
MLPHARE	phasing
CCP4	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2002-10-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Advisory, Data collection, Database references
• Version 1.4: 2023-01-25
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary