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- PDB-1pvq: BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pvq | |||||||||
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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 ENGINEERED RECOGNITION SITE LOXM7 | |||||||||
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![]() | RECOMBINATION/DNA / CRE / ![]() ![]() | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Baldwin, E.P. / Martin, S.S. / Abel, J. / Gelato, K.A. / Kim, H. / Schultz, P.G. / Santoro, S.W. | |||||||||
![]() | ![]() 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: ![]() Title: Directed evolution of the site specificity of Cre recombinase. Authors: Santoro, S.W. / Schultz, P.G. #2: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.8 KB | Display | ![]() |
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PDB format | ![]() | 139.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pvpC ![]() 1pvrC ![]() 1kbuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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. |
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Components
#1: DNA chain | Mass: 10469.798 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: TOP STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26) Source: (synth.) ![]() ![]() | ||
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#2: DNA chain | Mass: 10438.787 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: BOTTOM STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26) Source: (synth.) ![]() ![]() | ||
#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.) ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / 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![]() |
Reflection | Resolution: 2.75→90 Å / Num. all: 31227 / Num. obs: 29853 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3001 / % possible all: 97.8 |
Reflection | *PLUS % possible obs: 96 % |
Reflection shell | *PLUS % possible obs: 98 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KBU Resolution: 2.75→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 d res low obs: 5 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 5 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |