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Yorodumi- PDB-3ddv: The crystal structure of the transcriptional regulator (GntR fami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ddv | ||||||
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Title | The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583 | ||||||
Components | Transcriptional regulator (GntR family) | ||||||
Keywords | transcription regulator / Transcriptional regulator (GntR family / Structure genomics / PSI2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Zhang, R. / Zhou, M. / Bargassa, M. / Otwinowski, Z. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583 Authors: Zhang, R. / Zhou, M. / Bargassa, M. / Otwinowski, Z. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ddv.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ddv.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ddv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ddv_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 3ddv_full_validation.pdf.gz | 463.7 KB | Display | |
Data in XML | 3ddv_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3ddv_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/3ddv ftp://data.pdbj.org/pub/pdb/validation_reports/dd/3ddv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | This protein existed as dimer. The deposited MolA/MolB and MolC/MolD are two dimers in the asymmtric unit. |
-Components
#1: Protein | Mass: 16597.646 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: GI:29343357 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q835P8*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→80.06 Å / Num. all: 29406 / Num. obs: 28847 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 47.9 |
Reflection shell | Resolution: 2.65→2.718 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.88 / Num. unique all: 2253 / % possible all: 75.68 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→80.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.355 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.262 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 51.144 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→80.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.649→2.718 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.549 Å / Origin y: 28.111 Å / Origin z: 36.145 Å
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Refinement TLS group |
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