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Yorodumi- PDB-1t6a: Crystal Structure of Protein of Unknown Function from Bacillus st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6a | ||||||
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Title | Crystal Structure of Protein of Unknown Function from Bacillus stearothermophilus | ||||||
Components | RBSTP2229 gene product | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Bacillus stearothermophilus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Rbstp2229 protein / Rbstp2229 like protein / Protein of unknown function DUF1885 / Rbstp2229-like superfamily / Domain of unknown function (DUF1885) / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Osipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of hypothetical protein (RBSTP2229 gene product) from Bacillus stearothermophilus Authors: Osipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein was not deposited into any sequence database. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). The biological molecule for the protein is not known. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6a.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6a.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t6a_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 1t6a_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 1t6a_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1t6a_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6a ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6a | 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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Unit cell |
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Components on special symmetry positions |
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Details | the biological assembly unknown |
-Components
#1: Protein | Mass: 14134.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P84137 |
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#2: Chemical | ChemComp-NO3 / |
#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: 4.1 Å3/Da / Density % sol: 69.7 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Bis-Tris-Propane, Sodium Nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97952 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 12, 2004 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. all: 14861 / Num. obs: 14757 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.07 / Num. unique all: 1010 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 2.831 / SU ML: 0.075 / σ(F): 0 / ESU R: 0.131 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.053→2.106 Å / Total num. of bins used: 20
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