+Open data
-Basic information
Entry | Database: PDB / ID: 2oaa | ||||||
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Title | Restriction endonuclease MvaI-cognate DNA substrate complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / MONOMERIC ENDONUCLEASE / DNA SUBSTRATE COMPLEX / RESTRICTION ENZYME / MVAI / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Kocuria varians (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kaus-Drobek, M. / Czapinska, H. / Sokolowska, M. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, K. / Siksnys, V. / Bochtler, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Authors: Kaus-Drobek, M. / Czapinska, H. / Sokolowska, M. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M. #1: Journal: To be Published Title: Structural and Mechanistic Similarities between Restriction Endonucleases BcnI and MvaI and the DNA Repair Protein MutH 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 | 2oaa.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oaa.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/2oaa ftp://data.pdbj.org/pub/pdb/validation_reports/oa/2oaa | HTTPS FTP |
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-Related structure data
Related structure data | 2oa9SC 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
#1: DNA chain | Mass: 3389.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: T strand #2: DNA chain | Mass: 3318.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: A strand #3: Protein | Mass: 28702.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kocuria varians (bacteria) / Gene: mvaIR / Plasmid: pBAD24_R.MvaI / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8RNV5 #4: Chemical | ChemComp-CA / #5: 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: 2.19 Å3/Da / Density % sol: 43.81 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 0.1 M HEPES pH 7.89, 0.2 M CaCl2, 25 % PEG4000, pH 7.9, 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 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 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: 1.5→30 Å / Num. all: 94979 / Num. obs: 94979 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 13630 / Rsym value: 0.29 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OA9 Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.147 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: TLS refinement used. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Both Refmac and CNS are used for refinement
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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: 11.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 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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