2GZX | pdb_00002gzx

Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR237.

• PDB DOI: https://doi.org/10.2210/pdb2GZX/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Staphylococcus aureus subsp. aureus MW2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-12 Released: 2006-07-11 
• Deposition Author(s): Vorobiev, S.M., Neely, H., Seetharaman, J., Wang, D., Fang, Y., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.286 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Literature

Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR237.

Vorobiev, S.M., Neely, H., Seetharaman, J., Wang, D., Fang, Y., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 61.58 kDa 
• Atom Count: 4,104 
• Modeled Residue Count: 506 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative TatD related DNase	A, B	265	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 6  Gene Names: MW0446

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A], E [auth B], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.286 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.678	α = 90
b = 77.324	β = 98.01
c = 76.129	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Vorobiev, S.M., Neely, H., Seetharaman, J., Wang, D., Fang, Y., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary