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Yorodumi- PDB-4jcx: Crystal structure of the Restriction-Modification Controller Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jcx | ||||||
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Title | Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / helix-turn-helix / C controller protein / restriction-modification systems / transcriptional regulation / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Citrobacter sp. RFL231 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / Mcgeehan, J.E. / Kneale, G.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression. Authors: Shevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / Swiderska, A. / McGeehan, J.E. / Kneale, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jcx.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jcx.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jcx_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 4jcx_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 4jcx_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4jcx_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcx ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcx | HTTPS FTP |
-Related structure data
Related structure data | 4jcyC 4jqdC 3lfpS 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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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A PROTEIN DIMER BOUND TO DNA DUPLEX. |
-Components
#1: Protein | Mass: 11380.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter sp. RFL231 (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q32WH4 #2: DNA chain | | Mass: 6472.251 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 6409.153 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: 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: 2.32 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % ...Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % (w/v) PEG6K, protein dimer/DNA molar ratio 1:2, protein concentration 1.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.61 Å / Num. all: 14413 / Num. obs: 14402 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1642 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LFP Resolution: 2.3→50.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.887 / SU ML: 0.098 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 36.251 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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