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Yorodumi- PDB-4jg3: Crystal structure of catabolite repression control protein (crc) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jg3 | ||||||
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Title | Crystal structure of catabolite repression control protein (crc) from Pseudomonas aeruginosa | ||||||
Components | Catabolite repression control protein | ||||||
Keywords | UNKNOWN FUNCTION / AP endonuclease protein family | ||||||
Function / homology | Function and homology information double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Grishkovskaya, I. / Milojevic, T. / Sonnleitner, E. / Blaesi, U. / Djinovic-Carugo, K. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: The Pseudomonas aeruginosa Catabolite Repression Control Protein Crc Is Devoid of RNA Binding Activity Authors: Milojevic, T. / Grishkovskaya, I. / Sonnleitner, E. / Djinovic-Carugo, K. / Blasi, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jg3.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jg3.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 4jg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jg3_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 4jg3_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 4jg3_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4jg3_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jg3 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jg3 | HTTPS FTP |
-Related structure data
Related structure data | 2jc5S S: Starting model for refinement |
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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: 30101.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: crc / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)(pLysS / References: UniProt: Q51380 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 3.29 Å3/Da / Density % sol: 62.63 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10%(w/v) PEG1500, 40mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.59 Å / Num. all: 37275 / Num. obs: 37261 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2073 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2jc5 Resolution: 1.8→44.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.801 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / 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: 42.784 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.848 Å / Total num. of bins used: 20
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