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Yorodumi- PDB-2p14: Crystal structure of small subunit (R.BspD6I2) of the heterodimer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p14 | ||||||
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Title | Crystal structure of small subunit (R.BspD6I2) of the heterodimeric restriction endonuclease R.BspD6I | ||||||
Components | Heterodimeric restriction endonuclease R.BspD6I small subunit | ||||||
Keywords | HYDROLASE / heterodimeric restriction endonuclease | ||||||
Function / homology | Restriction Endonuclease - #50 / Restriction endonuclease, type II, AlwI / AlwI restriction endonuclease / Restriction Endonuclease / endonuclease activity / 3-Layer(aba) Sandwich / Alpha Beta / Heterodimeric restriction endonuclease R.BspD6I small subunit Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kachalova, G.S. / Bartunik, H.D. / Artyukh, R.I. / Rogulin, E.A. / Yunusova, A.K. / Zheleznaya, L.A. / Matvienko, N.I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. Authors: Kachalova, G.S. / Rogulin, E.A. / Yunusova, A.K. / Artyukh, R.I. / Perevyazova, T.A. / Matvienko, N.I. / Zheleznaya, L.A. / Bartunik, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p14.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p14.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 2p14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p14_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 2p14_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2p14_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2p14_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p14 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p14 | HTTPS FTP |
-Related structure data
Related structure data | 2ewfSC 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: 22508.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: D6 / Gene: bspD6IR2 / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A3FEV8, type II site-specific deoxyribonuclease | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 1.99 Å3/Da / Density % sol: 38.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 17, 2006 / Details: AU-COATED PLANAR and TOROIDAL MIRRORS |
Radiation | Monochromator: SI111 / 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→20 Å / Num. all: 29298 / Num. obs: 28430 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 2.91 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1428 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ewf Resolution: 1.5→10.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.399 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / 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: 18.891 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→10.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Total num. of bins used: 20
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