+Open data
-Basic information
Entry | Database: PDB / ID: 1pvi | ||||||
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Title | STRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E. | ||||||
Citation | Journal: EMBO J. / Year: 1994 Title: Structure of PvuII endonuclease with cognate DNA. Authors: Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E. #1: Journal: Proteins / Year: 1994 Title: Expression, Purification, and Crystallization of Restriction Endonuclease PvuII with DNA Containing its Recognition Site Authors: Balendiran, K. / Bonventre, J. / Knott, R. / Jack, W. / Benner, J. / Schildkraut, I. / Anderson, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvi.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvi.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvi ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvi | HTTPS FTP |
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-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
#1: DNA chain | Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 18370.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Proteus vulgaris (bacteria) / References: UniProt: P23657 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 K / pH: 4.5 / Method: vapor diffusion, hanging dropDetails: Balendiran, K., (1994) Proteins: Struct.,Funct., Genet., 19, 77. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Redundancy: 4.4 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Num. obs: 10282 / % possible obs: 92.7 % / Redundancy: 4.4 % / Num. measured all: 45607 / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Resolution: 2.6→10 Å
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / Total num. of bins used: 5 |