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Yorodumi- PDB-2q10: RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q10 | ||||||
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Title | RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / BCNI / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacillus centrosporus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA. Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M. #1: Journal: To be Published Title: Restriction Endonucleases that Resemble a Component of the Bacterial DNA Repair Machinery Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Siksnys, V. / Bochtler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q10.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q10.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 2q10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q10 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q10 | HTTPS FTP |
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-Related structure data
Related structure data | 2odhC 2odiSC 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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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules CEDF
#1: DNA chain | Mass: 3352.214 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3356.182 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 27334.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus centrosporus (bacteria) / Gene: bcnIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 / References: UniProt: Q8RNV8 |
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-Non-polymers , 3 types, 650 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.05 Å3/Da / Density % sol: 40.07 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.02 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, 30% (V/V) 2-METHYL-2,4-PENTANEDIOL , pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2006 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 57635 / Num. obs: 57635 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8336 / Rsym value: 0.26 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ODI Resolution: 1.75→29.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.451 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: TLS REFINEMENT HAVE BEEN USED. 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.72 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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