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- PDB-1rve: THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rve | ||||||
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Title | THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS | ||||||
![]() | ENDONUCLEASE EcoR V | ||||||
![]() | ENDONUCLEASE | ||||||
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 | ![]() | ||||||
![]() | Winkler, F.K. | ||||||
![]() | ![]() Title: The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate 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. #1: ![]() Title: Structure and Function of Restriction Endonucleases Authors: Winkler, F.K. #2: ![]() Title: Crystallization of Complexes of EcoRV Endonuclease with Cognate and Non-Cognate DNA Fragments Authors: Winkler, F.K. / D'Arcy, A. / Bloecker, H. / Frank, R. / Van Boom, J.H. #3: ![]() Title: Purification and Crystallization of the EcoRV Restriction Endonuclease Authors: D'Arcy, A. / Brown, R.S. / Zabeau, M. / Van Resandt, R.W. / Winkler, F.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: RESIDUES PRO A 73 AND PRO B 73 ARE CIS PROLINES. 2: THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY (THEY WERE INCLUDED IN THE REFINEMENT AND ARE ENTERED WITH UNIT OCCUPANCIES): A CHAIN: GLN 68, GLN 69, ASN 70, LYS 245 B CHAIN: LYS 161 |
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Components
#1: Protein | Mass: 28690.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P04390, type II site-specific deoxyribonuclease #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / PH range low: 7.8 / PH range high: 7 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 16509 / Num. measured all: 86437 / Rmerge(I) obs: 0.069 |
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Processing
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Refinement | Resolution: 2.5→8 Å / σ(F): 0 Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND ARE ENTERED WITH ZERO OCCUPANCIES. THE CORRESPONDING B FACTORS ARE MEANINGLESS. THE COORDINATES OF THE ATOMS OF THESE SEGMENTS ...Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND ARE ENTERED WITH ZERO OCCUPANCIES. THE CORRESPONDING B FACTORS ARE MEANINGLESS. THE COORDINATES OF THE ATOMS OF THESE SEGMENTS HAVE BEEN PRODUCED THROUGH THE INITIAL MOLECULAR DYNAMICS RUNS STARTING WITH ARBITRARY CONFORMATIONS AND UNIT OCCUPANCIES. THE DENSITY IN THESE REGIONS IS MOSTLY WEAK AND FRAGMENTED. THE RESIDUES HAVE BEEN LEFT IN THIS COORDINATE FILE JUST TO DELINEATE THE APPROXIMATE PATH OF THE CHAIN IN THESE REGIONS. THEY WERE INCLUDED WITH ZERO OCCUPANCIES IN TNT REFINEMENT TO MAINTAIN REASONABLE STEREOCHEMISTRY. A 13 TO A 17 B 13 TO B 19 A 142 TO A 148 B 142 TO B 148 A 183 TO A 187 B 183 TO B 187 A 221 TO A 228 B 221 TO B 228 THE FOLLOWING PROTEIN SIDE CHAINS HAVE NO OR POORLY DEFINED DENSITY (THEY WERE INCLUDED IN THE REFINEMENT AND ARE ENTERED WITH UNIT OCCUPANCIES): A CHAIN: GLN 68, GLN 69, ASN 70, LYS 245 B CHAIN: LYS 161
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection all: 15963 / σ(F): 0 / Rfactor all: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.07 |