1XWY | pdb_00001xwy

Crystal structure of tatD deoxyribonuclease from Escherichia coli K12 at 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1XWY/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2004-11-02 Released: 2005-01-25 
• Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tatD DNase from Escherichia coli at 2.0 A resolution

Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C.

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: 29.65 kDa 
• Atom Count: 2,340 
• Modeled Residue Count: 260 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonuclease tatD	A	264	Escherichia coli	Mutation(s): 0  Gene Names: tatD, mttC EC: 3.1.21 (PDB Primary Data), 3.1.13 (UniProt), 3.1.11 (UniProt)
UniProt
Find proteins for P27859 (Escherichia coli (strain K12)) Explore P27859  Go to UniProtKB:  P27859

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.885	α = 90
b = 73.885	β = 90
c = 67.824	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description