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- PDB-1rvb: MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTAL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rvb | ||||||
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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 | ||||||
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![]() | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Kostrewa, D. / Winkler, F.K. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Structure and Function of Restriction Endonucleases Authors: Winkler, F.K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.4 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.4 KB | Display | ![]() |
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Full document | ![]() | 444 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 73 / 2: CIS PROLINE - PRO B 73 |
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Components
#1: DNA chain | Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 28559.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.09 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 26271 / % possible obs: 83.7 % / Num. measured all: 40175 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 65 % |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.165 / Rfactor Rwork: 0.165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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