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Yorodumi- PDB-2ek0: Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ek0 | ||||||
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Title | Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form | ||||||
Components | Stage V sporulation protein S (SpoVS) related protein | ||||||
Keywords | METAL BINDING PROTEIN / Sporulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form Authors: Rehse, P.H. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ek0.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ek0.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ek0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/2ek0 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/2ek0 | HTTPS FTP |
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-Related structure data
Related structure data | 2eh1S S: Starting model for refinement |
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Similar structure data | |
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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9695.244 Da / Num. of mol.: 2 / Mutation: K22M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SK02 #2: Chemical | #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: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 100mM Na cacodylate, 0.2M Zn Acetate, 35% PEG 200 , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→40.5 Å / Num. all: 14849 / Num. obs: 14671 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.066 / Χ2: 1 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.49 / Num. unique all: 1357 / Χ2: 1 / % possible all: 92.6 |
-Phasing
Phasing MR | Rfactor: 0.448 / Cor.coef. Fo:Fc: 0.574
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EH1 Resolution: 1.9→40.46 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 94.256 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.964 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→40.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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Xplor file |
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