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Yorodumi- PDB-4mqd: Crystal structure of ComJ, inhibitor of the DNA degrading activit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mqd | ||||||
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Title | Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis | ||||||
Components | DNA-entry nuclease inhibitor | ||||||
Keywords | Hydrolase Inhibitor / inhibitor of NucA / Competence protein J / Midwest center for structural genomics / MCSG / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å | ||||||
Authors | Chang, C. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis Authors: Chang, C. / Mack, J. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mqd.cif.gz | 229.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mqd.ent.gz | 195 KB | Display | PDB format |
PDBx/mmJSON format | 4mqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/4mqd ftp://data.pdbj.org/pub/pdb/validation_reports/mq/4mqd | 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | A and B, C and D from PISA |
-Components
#1: Protein | Mass: 15472.742 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: nin, comJ, BSU03420 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pGrow7-K / References: UniProt: P12669 #2: 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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M sodium acetate pH 4.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-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 315r / Detector: CCD / Date: Feb 7, 2013 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 35143 / Num. obs: 35026 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 1.54 / Num. unique all: 1786 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.16→41.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.221 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.225 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 141.42 Å2 / Biso mean: 36.687 Å2 / Biso min: 11.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→41.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.156→2.212 Å / Total num. of bins used: 20
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