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Yorodumi- PDB-1rvc: MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rvc | ||||||
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Title | MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION | ||||||
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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Kostrewa, D. / Winkler, F.K. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. Authors: Kostrewa, D. / Winkler, F.K. #1: Journal: Embo J. / Year: 1993 Title: The Crystal Structure of EcoRV Endonuclease and of its Complexes with Cognate and Noncognate DNA Fragments Authors: Winkler, F.K. / Banner, D.W. / Oefner, C. / Tsernoglou, D. / Brown, R.S. / Heathman, S.P. / Bryan, R.K. / Martin, P.D. / Petratos, K. / Wilson, K.S. #2: Journal: Curr.Opin.Struct.Biol. / Year: 1992 Title: Structure and Function of Restriction Endonucleases Authors: Winkler, F.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rvc.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rvc.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rvc ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rvc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1841.268 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 1470.010 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 28559.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P04390 #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Num. obs: 26657 / % possible obs: 85.1 % / Num. measured all: 39654 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 57.4 % |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.156 / Rfactor Rwork: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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