[English] 日本語
Yorodumi- PDB-1gdr: MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gdr | ||||||
---|---|---|---|---|---|---|---|
Title | MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS | ||||||
Components | GAMMA DELTA-RESOLVASE | ||||||
Keywords | SITE-SPECIFIC RECOMBINASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.5 Å | ||||||
Authors | Rice, P.A. / Steitz, T.A. | ||||||
Citation | Journal: EMBO J. / Year: 1994 Title: Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. Authors: Rice, P.A. / Steitz, T.A. #1: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: The Crystal Structure of the Catalytic Domain of the Site Specific Recombination Enzyme Gd Resolvase at 2.7 Resolution Authors: Sanderson, M.R. / Freemont, P.S. / Rice, P.A. / Goldman, A. / Hatfull, G.F. / Grindley, N.D.F. #2: Journal: J.Biol.Chem. / Year: 1986 Title: Preliminary X-Ray Diffraction Studies of the Putative Catalytic Domain of Gd Resolvase from Escherichia Coli Authors: Abdel-Meguid, S.S. / Murthy, H.M.K. / Steitz, T.A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984 Title: Cleavage of the Site-Specific Recombination Protein Gd Resolvase: The Smaller of Two Fragments Binds DNA Specifically Authors: Abdel-Muguid, S.S. / Grindley, N.D.F. / Templeton, N.S. / Steitz, T.A. #4: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallization of Resolvase, a Repressor that Also Catalyzes Site-Specific DNA Recombination Authors: Weber, P.C. / Ollis, D.L. / Bebrin, W.R. / Abdel-Meguid, S.S. / Steitz, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gdr.cif.gz | 14 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gdr.ent.gz | 6.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gdr_validation.pdf.gz | 338.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gdr_full_validation.pdf.gz | 338.6 KB | Display | |
Data in XML | 1gdr_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 1gdr_validation.cif.gz | 2.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/1gdr ftp://data.pdbj.org/pub/pdb/validation_reports/gd/1gdr | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THE MATRIX GIVEN BELOW WILL APPROXIMATELY SUPERIMPOSE MONOMER-B FROM THE C2221 CRYSTAL STRUCTURE ONTO THE THE STRUCTURE PRESENTED IN THIS ENTRY. 0.77672 0.02093 -0.62949 (X - 25.22352) + -9.96070 0.62967 -0.00232 0.77686 (X - 53.97461) + 43.29039 0.01480 -0.99978 -0.01498 (X - 47.00185) + 12.88526 |
-Components
#1: Protein | Mass: 15515.833 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P03012 |
---|---|
Compound details | THESE CRYSTALS DO NOT DIFFRACT AS WELL AS THE C2221 CRYSTAL FORM (PDB ENTRY 2RSL) AND ARE MAINLY OF ...THESE CRYSTALS DO NOT DIFFRACT AS WELL AS THE C2221 CRYSTAL FORM (PDB ENTRY 2RSL) AND ARE MAINLY OF INTEREST IN REGARDS TO CRYSTAL PACKING. THE AUTHORS HAVE PROPOSED A MODEL OF THE SYNAPTIC COMPLEX BASED ON THE PACKING OF PROTOMERS IN THIS UNIT CELL. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 30 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / Num. obs: 3455 / % possible obs: 85 % / Rmerge(I) obs: 0.049 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.31 / Rfactor obs: 0.31 / Highest resolution: 3.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.5 Å / Rfactor obs: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.55 |