+Open data
-Basic information
Entry | Database: PDB / ID: 1nzb | ||||||
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Title | Crystal structure of wild type Cre recombinase-loxP synapse | ||||||
Components |
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Keywords | REPLICATION/DNA / Cre / recombinase / DNA / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Ennifar, E. / Meyer, J.E.W. / Buchholz, F. / Stewart, A.F. / Suck, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2003 Title: Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation Authors: Ennifar, E. / Meyer, J.E.W. / Buchholz, F. / Stewart, A.F. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzb.cif.gz | 343.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzb.ent.gz | 270.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzb ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzb | HTTPS FTP |
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-Related structure data
Related structure data | 1ouqC 1q3uC 1q3vC 1crxS C: citing same article (ref.) S: Starting model for refinement |
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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 | dimeric Cre recombinase bound to a double stranded DNA loxP site |
-Components
-DNA chain , 2 types, 4 molecules CGDH
#1: DNA chain | Mass: 11364.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: First strand of loxP site #2: DNA chain | Mass: 11387.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Second strand of loxP site |
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-Protein , 1 types, 4 molecules ABEF
#3: Protein | Mass: 38595.164 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Plasmid: pGem / Production host: Escherichia coli (E. coli) / References: UniProt: P06956 |
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-Non-polymers , 3 types, 15 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: NaCl, EDTQ, Glycerol, HEPES, MgCl2, PEG 2000, MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 1999 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→100 Å / Num. all: 120449 / Num. obs: 116497 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.095 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.1→3.28 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.278 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 1CRX Resolution: 3.1→8 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.1965 Å2 / ksol: 0.370259 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.46 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.28 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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