+Open data
-Basic information
Entry | Database: PDB / ID: 6ekr | |||||||||
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Title | Crystal structure of Type IIP restriction endonuclease Kpn2I | |||||||||
Components | Type ii site-specific deoxyribonuclease | |||||||||
Keywords | HYDROLASE / Restriction endonuclease / PD-(D/E)xK nuclease | |||||||||
Function / homology | type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / Type ii site-specific deoxyribonuclease Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å | |||||||||
Authors | Tamulaitiene, G. / Manakova, E. / Grazulis, S. / Siksnys, V. | |||||||||
Funding support | Lithuania, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA Authors: Tamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Grazulis, S. / Siksnys, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ekr.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ekr.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ekr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ekr_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 6ekr_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 6ekr_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 6ekr_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6ekr ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6ekr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36329.820 Da / Num. of mol.: 1 / Mutation: K185A,K187A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: Q93K38, type II site-specific deoxyribonuclease | ||
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#2: Chemical | ChemComp-SO4 / #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: 2.93 Å3/Da / Density % sol: 57.97 % / Description: small cubic crystals (30-50 mkm) |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystallization buffer: 0.1M NaHepes pH7.5, 1.4M ammonium sulfate and glycerol 10%. Complex of Kpn2I with DNA was used at concentration 2-7.5mg/ml PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98019,0.98029,0.97789 | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.88→95.31 Å / Num. obs: 9398 / % possible obs: 100 % / Redundancy: 39.8 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.021 / Rrim(I) all: 0.134 / Rsym value: 0.116 / Net I/σ(I): 28.3 | ||||||||||||
Reflection shell | Resolution: 2.88→3.04 Å / Redundancy: 34.6 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1347 / Rpim(I) all: 0.093 / Rrim(I) all: 0.555 / Rsym value: 0.537 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: FREE R-VALUE / ESU R Free: 0.432 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.086 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.88→20 Å
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Refine LS restraints |
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