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Yorodumi- PDB-2gen: Structural Genomics, the crystal structure of a probable transcri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gen | ||||||
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Title | Structural Genomics, the crystal structure of a probable transcriptional regulator from Pseudomonas aeruginosa PAO1 | ||||||
Components | probable transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / APC6095 / Pseudomonas aeruginosa PA01 / TetR family / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Tan, K. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a probable transcriptional regulator from Pseudomonas aeruginosa PAO1 Authors: Tan, K. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE MOLECULE CAN EXIST IN BOTH MONOMERIC AND DIMERIC FORMS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE DIMERIC FORM. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gen.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gen.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gen_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2gen_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 2gen_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2gen_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/2gen ftp://data.pdbj.org/pub/pdb/validation_reports/ge/2gen | 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 is a dimer. In the crystal structure, there is one monomer in one asymmetric unit. The other pairing monomer can be generated by a symmetry operation of (-X+1,-Y,Z). |
-Components
#1: Protein | Mass: 21827.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: 15597033 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I2Q9 |
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#2: 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: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.2M di-Ammonium Tartrate, 0.1M NaAcetate, pH 4.6, 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: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→18.03 Å / Num. all: 26394 / Num. obs: 26275 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 27.52 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.45 / Num. unique all: 2588 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→18.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.038 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / 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: 30.167 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→18.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 Å / Total num. of bins used: 20
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