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Yorodumi- PDB-3f52: Crystal structure of the clp gene regulator ClgR from C. glutamicum -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f52 | ||||||
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Title | Crystal structure of the clp gene regulator ClgR from C. glutamicum | ||||||
Components | clp gene regulator (ClgR) | ||||||
Keywords | TRANSCRIPTION ACTIVATOR / gene regulator / helix-turn-helix motif / transcriptional activator / human pathogen | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Russo, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes Authors: Russo, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f52.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f52.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 3f52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f52 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f52 | HTTPS FTP |
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-Related structure data
Related structure data | 3f51SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12647.396 Da / Num. of mol.: 2 / Fragment: clgr_c Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg2152, Cgl1962 / Plasmid: pEKEx1 / Production host: Escherichia coli (E. coli) / Strain (production host): BB1553 / References: UniProt: Q8NP59 #2: Chemical | ChemComp-GOL / #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: 1.94 Å3/Da / Density % sol: 36.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M HEPES, 8.5% PEG 8000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0685 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2008 |
Radiation | Monochromator: sagitally focused Si(111), bending mirror for vertical focusing, spot size 20x50um Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0685 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42 Å / Num. all: 20944 / Num. obs: 20938 / % possible obs: 100 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 10 % / Rsym value: 0.057 / Net I/σ(I): 24.56 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2.56 / Num. unique all: 3143 / Rsym value: 0.799 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F51 Resolution: 1.75→41.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.273 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.7 / σ(I): 3 / ESU R: 0.098 / ESU R Free: 0.097 / 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: 33.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→41.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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