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Yorodumi- PDB-1wv3: Crystal structure of N-terminal domain of hypothetical protein SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wv3 | ||||||
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Title | Crystal structure of N-terminal domain of hypothetical protein SAV0287 from Staphylococcus aureus | ||||||
Components | similar to DNA segregation ATPase and related proteins | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ATPase | ||||||
Function / homology | Function and homology information : / membrane => GO:0016020 / DNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Tanaka, Y. / Yasutake, Y. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Crystal structure analysis reveals a novel forkhead-associated domain of ESAT-6 secretion system C protein in Staphylococcus aureus. Authors: Tanaka, Y. / Kuroda, M. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Watanabe, N. / Ohta, T. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wv3.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wv3.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wv3_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 1wv3_full_validation.pdf.gz | 432.2 KB | Display | |
Data in XML | 1wv3_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1wv3_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wv3 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wv3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27960.383 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Species: Staphylococcus aureus / Strain: Mu50 / ATCC 700699 / Gene: SAV0287 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8NYF3 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Bis-Tris, PEG3350, Magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97938 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2004 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97938 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 27431 / Num. obs: 27431 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.147 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Num. unique all: 2697 / Rsym value: 0.313 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.1368 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å
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