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Open data
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Basic information
Entry | Database: PDB / ID: 1kbu | ||||||
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Title | CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION | ||||||
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![]() | HYDROLASE / LIGASE/DNA / SITE-SPECIFIC RECOMBINASE / HOLLIDAY JUNCTION COMPLEX / DNA-PROTEIN CO-CRYSTAL / INT RECOMBINASE MECHANISM / LIGASE-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Martin, S.S. / Pulido, E. / Chu, V.C. / Lechner, T. / Baldwin, E.P. | ||||||
![]() | ![]() 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. #1: ![]() Title: Structure of the Holliday Junction Intermediate in Cre-loxP Site-Specific Recombination Authors: Gopaul, D.N. / Guo, F. / van Duyne, G.D. #2: ![]() Title: Quasi-Equivalence in Site-Specific Recombinase Structure and Function: Crystal Structure and Activity of Trimeric Cre Recombinase Bound to a Three-Way Lox DNA Junction Authors: Woods, K.C. / Martin, S.S. / Chu, V.C. / Baldwin, E.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.2 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.7 KB | Display | ![]() |
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Full document | ![]() | 527.2 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 BIOLOGICAL ASSEMBLY IS A CRE TETRAMER BOUND TO TWO LOXP SITES, GENERATED FROM THE ASYMMETRIC UNIT BY THE CRYSTALLOGRAPHIC TWO-FOLD AXIS PLUS TRANSLATIONS: x, -y+1, -z+1 |
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Components
#1: DNA chain | Mass: 10510.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction | ||
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#2: DNA chain | Mass: 10399.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: part of Holliday junction / References: GenBank: 215626 | ||
#3: Protein | Mass: 39424.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LYS86 AND LYS201 INTERACTIONS WITH THE SCISSILE BASE SUGGEST HOW STRAND EXCHANGE ORDER IS DETERMINED Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: MPD, sodium acetate, calcium chloride, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21-25 ℃ / pH: 7 / Method: vapor diffusion / 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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2000 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.5 Å / Num. all: 53608 / Num. obs: 53320 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.037 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7169 / Rsym value: 0.287 / % possible all: 89.8 |
Reflection | *PLUS Num. obs: 44903 / % possible obs: 89 % / Num. measured all: 161433 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS Rmerge(I) obs: 0.287 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT Starting model: combination of 1CRX and 4CRX (see publication for details) Resolution: 2.2→5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: NONE | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å /
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Refinement | *PLUS Lowest resolution: 5 Å / Num. reflection obs: 45726 / Num. reflection Rfree: 2441 / % reflection Rfree: 4 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.61 |