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Yorodumi- PDB-2i9x: Structural Genomics, the crystal structure of SpoVG conserved dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i9x | ||||||
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Title | Structural Genomics, the crystal structure of SpoVG conserved domain from Staphylococcus epidermidis ATCC 12228 | ||||||
Components | Putative septation protein spoVGSeptum | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86317.1 / SpoVG / Staphylococcus epidermidis ATCC 12228 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information division septum assembly / sporulation resulting in formation of a cellular spore Similarity search - Function | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Tan, K. / Maltseva, N. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of SpoVG from Staphylococcus epidermidis ATCC 12228 Authors: Tan, K. / Maltseva, N. / Bargassa, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i9x.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i9x.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 2i9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/2i9x ftp://data.pdbj.org/pub/pdb/validation_reports/i9/2i9x | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10096.718 Da / Num. of mol.: 2 / Fragment: conserved domain residues 1-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: spoVG, SE_2285 / Plasmid: PMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8CML1 #2: Chemical | ChemComp-EDO / #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: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5%(w/v) isopropanol, 0.1M HEPES pH 7.5, 10%(v/w) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 2, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→26.51 Å / Num. all: 19791 / Num. obs: 19791 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.62 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.73 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.229 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.952 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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