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Yorodumi- PDB-3hqf: Crystal structure of restriction endonuclease EcoRII N-terminal e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hqf | ||||||
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Title | Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / restriction endonuclease / EcoRII / DNA-binding pseudobarrel fold / protein-DNA complex / DNA recognition / Endonuclease / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å | ||||||
Authors | Golovenko, D. / Manakova, E. / Grazulis, S. / Tamulaitiene, G. / Siksnys, V. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Authors: Golovenko, D. / Manakova, E. / Tamulaitiene, G. / Grazulis, S. / Siksnys, V. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold Authors: Zhou, X.E. / Wang, Y. / Reuter, M. / Mucke, M. / Kruger, D.H. / Meehan, E.J. / Chen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hqf.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hqf.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 3hqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqf ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqf | HTTPS FTP |
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-Related structure data
Related structure data | 3hqgC 1na6S 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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-Components
#1: Protein | Mass: 19909.236 Da / Num. of mol.: 1 Fragment: N-terminal effector-binding domain (UNP residues 2-170) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EcoRII / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 References: UniProt: O69414, type II site-specific deoxyribonuclease |
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#2: DNA chain | Mass: 2732.786 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2741.800 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: 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: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1M sodium acetate, 0.2M lithium acetate, 10% glycerol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2006 |
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 2.504→63.5 Å / Num. obs: 9055 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.856 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 7 / Num. measured all: 7469 / Num. unique all: 1199 / Rsym value: 0.079 / % possible all: 94.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.541 / Cor.coef. Fo:Fc: 0.234 / Cor.coef. Io to Ic: 0.252
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NA6 Resolution: 2.51→17.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.859 / SU B: 16.833 / SU ML: 0.173 / SU R Cruickshank DPI: 0.794 / SU Rfree: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.794 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 69.12 Å2 / Biso mean: 14.983 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→17.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.505→2.569 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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