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Yorodumi- PDB-2gnp: Structural Genomics, the crystal structure of a transcriptional r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gnp | ||||||
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Title | Structural Genomics, the crystal structure of a transcriptional regulator from Streptococcus pneumoniae TIGR4 | ||||||
Components | transcriptional regulatorTranscriptional regulation | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / APC84799 / Streptococcus pneumoniae TIGR4 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Tan, K. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a transcriptional regulator from Streptococcus pneumoniae TIGR4 Authors: Tan, K. / Duggan, E. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gnp.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gnp.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gnp ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gnp | 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: 30465.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 14971716, UniProt: A0A0H2UN73*PLUS |
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#2: Chemical | ChemComp-PEG / |
#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: 2.08 Å3/Da / Density % sol: 40.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium Acetate, 0.1M MES, 30% PEG 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30.4 Å / Num. all: 30578 / Num. obs: 30578 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 20.81 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 30.39 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.57 / Num. unique all: 3047 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→30.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.105 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / 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: 21.637 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→30.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.648→1.691 Å / Total num. of bins used: 20
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