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Yorodumi- PDB-2g7s: The crystal structure of transcriptional regulator, TetR family, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g7s | ||||||
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Title | The crystal structure of transcriptional regulator, TetR family, from Agrobacterium tumefaciens | ||||||
Components | transcriptional regulator, TetR family | ||||||
Keywords | TRANSCRIPTION / APC5906 / TetR / PSI / Protein structure initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Lunin, V.V. / Chang, C. / Xu, X. / Gu, J. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of transcriptional regulator, TetR family, from Agrobacterium tumefaciens Authors: Lunin, V.V. / Chang, C. / Xu, X. / Gu, J. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g7s.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g7s.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g7s_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 2g7s_full_validation.pdf.gz | 429.3 KB | Display | |
Data in XML | 2g7s_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2g7s_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g7s ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g7s | 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 | Biological assembly is a dimer, formed by a molecule from the asymmetric unit plus (-x, -y, z) symmetry-related molecule |
-Components
#1: Protein | Mass: 21334.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 17738610, UniProt: A9CKG4*PLUS |
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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: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.5M K3PO4,0.5M Na3PO4 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793164 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793164 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 38903 / Num. obs: 38903 / % possible obs: 99.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.9 % / Rsym value: 0.085 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.506 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.779 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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