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Yorodumi- PDB-2hiy: The structure of conserved bacterial protein SP0830 from Streptoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hiy | ||||||
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Title | The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. (CASP Target) | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / COG3797 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | bacterial protein sp0830 like / SP0830-like domains / Protein of unknown function DUF1697 / Protein of unknown function (DUF1697) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Cuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. (CASP Target) Authors: Cuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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Remark 300 | Author states that biological unit for the protein is not yet known and is most likely a monomer |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hiy.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hiy.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hiy ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hiy | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 21371.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0830 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97RI5, UniProt: A0A0H2UPL4*PLUS #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: 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: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH8.5, 0.2M MgCl2, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97906, 0.97923 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2005 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→48.28 Å / Num. all: 160902 / Num. obs: 160902 / % possible obs: 98.23 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | |||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→48.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.711 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.062 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 20.701 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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