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Yorodumi- PDB-1pvr: BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvr | ||||||
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Title | BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE LOXP (WILDTYPE) RECOGNITION SITE | ||||||
Components |
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Keywords | RECOMBINATION/DNA / CRE / Recombinase / DNA / CRE-LOXP RECOMBINATION / RECOMBINATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å | ||||||
Authors | Baldwin, E.P. / Martin, S.S. / Abel, J. / Gelato, K.A. / Kim, H. / Schultz, P.G. / Santoro, S.W. | ||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water. Authors: Baldwin, E.P. / Martin, S.S. / Abel, J. / Gelato, K.A. / Kim, H. / Schultz, P.G. / Santoro, S.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Directed evolution of the site specificity of Cre recombinase. Authors: Santoro, S.W. / Schultz, P.G. #2: Journal: Biochemistry / Year: 2003 Title: Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination. Authors: Martin, S.S. / Chu, V.C. / Baldwin, E. #3: Journal: J.Mol.Biol. / Year: 2002 Title: The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex. Authors: Martin, S.S. / Pulido, E. / Chu, V.C. / Lechner, T.S. / Baldwin, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvr.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvr.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pvr_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 1pvr_full_validation.pdf.gz | 520 KB | Display | |
Data in XML | 1pvr_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 1pvr_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvr ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvr | HTTPS FTP |
-Related structure data
Related structure data | 1pvpC 1pvqC 1kbuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the tetrameric biological assembly is generated by the two fold axis: x, -y+1, -z+1. |
-Components
#1: DNA chain | Mass: 10470.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TOP STRAND OF LOXP WILDTYPE DNA SUBSTRATE / References: GenBank: 215623 | ||
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#2: DNA chain | Mass: 10439.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BOTTOM STRAND OF LOXP WILDTYPE DNA SUBSTRATE / References: GenBank: 215626 | ||
#3: Protein | Mass: 39222.805 Da / Num. of mol.: 2 / Mutation: I174L,T258N,R259S,E262G,E266G Source method: isolated from a genetically manipulated source Details: SELECTED CRE SITE-SPECIFIC RECOMBINASE MUTANT (I174L,T258N, R259S, E262G, E266G) Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / Plasmid: PET28B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P06956 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.09 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium Acetate, Calcium Chloride, 2,4-Methylpentanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21-25 ℃ / Method: vapor diffusion / Details: Martin, S.S., (2002) J.Mol.Biol., 319, 107. / PH range low: 5.5 / PH range high: 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 12, 2002 |
Radiation | Monochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→90 Å / Num. obs: 33418 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.65→2.74 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3364 / % possible all: 98.7 |
Reflection | *PLUS % possible obs: 97 % |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1KBU Resolution: 2.65→5 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a obs: 0.25 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→5 Å
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Refine LS restraints |
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