2GZX

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.286
R-Value Work: 0.258
R-Value Observed: 0.258

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for A0A0H3JV42 (Staphylococcus aureus (strain MW2)) Explore A0A0H3JV42 Go to UniProtKB: A0A0H3JV42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3JV42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.258
R-Value Observed: 0.258
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

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Entry History

Deposition Data

Released Date: 2006-07-11

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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

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Help and Resources

2GZX

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)