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Yorodumi- PDB-2gzx: Crystal Structure of the TatD deoxyribonuclease MW0446 from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gzx | ||||||
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Title | Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR237. | ||||||
Components | putative TatD related DNase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / TatD / DNase / deoxyribonuclease / NESG / ZR237 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR237. Authors: Vorobiev, S.M. / Neely, H. / Seetharaman, J. / Wang, D. / Fang, Y. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gzx.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gzx.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gzx_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 2gzx_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 2gzx_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 2gzx_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gzx ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gzx | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | monomer according to aggregation screening |
-Components
#1: Protein | Mass: 30672.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: MW2 / Gene: MW0446 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q1Y6Z0, UniProt: A0A0H3JV42*PLUS #2: Chemical | ChemComp-NI / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.2 Ammonium acetate, 5 mM magnesium chloride, 0.1 M TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→26.79 Å / Num. all: 53584 / Num. obs: 53477 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.548 / Num. unique all: 5328 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→26.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 307133.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.4446 Å2 / ksol: 0.338969 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→26.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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