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Yorodumi- PDB-3gv0: Crystal structure of LacI family transcription regulator from Agr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gv0 | ||||||
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Title | Crystal structure of LacI family transcription regulator from Agrobacterium tumefaciens | ||||||
Components | Transcriptional regulator, LacI familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION REGULATOR / PSI-II / 11224e / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / New York Structural GenomiX Research Consortium / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Bagaria, A. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of LacI family transcription regulator from Agrobacterium tumefaciens Authors: Bagaria, A. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gv0.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gv0.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gv0 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gv0 | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32427.455 Da / Num. of mol.: 1 / Fragment: UNP residues 62-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: AGR_C_2807, Atu1522 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7CZ24 |
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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: 3.72 Å3/Da / Density % sol: 66.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→43.36 Å / Num. all: 20658 / Num. obs: 20658 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 52.69 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 4.8 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→43.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.991 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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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: 46.203 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→43.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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