[English] 日本語
Yorodumi- PDB-4rve: THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rve | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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 / SYNCHROTRON / Resolution: 3 Å | ||||||
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. / Wilso, K.S. | ||||||
Citation | Journal: EMBO J. / Year: 1993 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: Journal: Curr.Opin.Struct.Biol. / Year: 1992 Title: Structure and Function of Restriction Endonucleases Authors: Winkler, F.K. #2: Journal: J.Mol.Biol. / Year: 1991 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rve.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rve.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rve ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rve | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO A 73, PRO B 73, AND PRO C 73 ARE CIS PROLINES. |
-Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 3 / Source method: obtained synthetically #2: Protein | Mass: 28559.158 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P04390 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.53 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Winkler, F.K., (1991) J.Mol.Biol., 217, 235. / PH range low: 6.9 / PH range high: 6.4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 |
---|---|
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 3 Å / Num. obs: 15231 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 15988 / % possible obs: 90 % / Rmerge(I) obs: 0.073 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3→8 Å Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND THE ATOMS AS FAR AS PRESENT ARE ENTERED WITH ZERO OCCUPANCIES AND B FACTORS OF 99.0. WITH THE EXCEPTION OF THE C-TERMINAL ...Details: THE CHAIN SEGMENTS LISTED BELOW APPEAR TO BE DISOREDERED AND THE ATOMS AS FAR AS PRESENT ARE ENTERED WITH ZERO OCCUPANCIES AND B FACTORS OF 99.0. WITH THE EXCEPTION OF THE C-TERMINAL RESIDUES 242-245, COORDINATES FOR THESE ILL-DEFINED 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 STRUCTURES PRESENT FOR THESE SEGMENTS IN THIS COORDINATE FILE ARE ONLY MEANT TO DELINEATE THE APPROXIMATE PATH OF THESE DISORDERED CHAIN SEGMENTS. IN THE FINAL TNT REFINEMENT ROUNDS THE CORRESPONDING ATOMS WERE INCLUDED WITH ZERO OCCUPANCIES TO MAINTAIN A REASONABLE STEREOCHEMISTRY. A 13 TO A 17 B 13 TO B 18 C 13 TO C 18 A 83 A 99 TO A 100 A 141 TO A 149 B 141 TO B 148 C 141 TO C 149 A 222 TO A 228 B 222 TO B 228 C 222 TO C 228 A 242 TO A 245 B 242 TO B 245 C 242 TO C 245 THE ATOMS OF A NUMBER OF SIDE CHAINS WITH POORLY DEFINED DENSITY ARE MARKED IN THE SAME WAY AND ARE: SUBUNIT A: GLU 57 B: LYS 67 C: GLU 57 LYS 98 ASN 70 LYS 85 LYS 85 LYS 98 LYS 98 GLU 99 GLU 99 ASN 100 GLU 101 LYS 102
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|