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Yorodumi- PDB-1s6m: Conjugative Relaxase Trwc In Complex With Orit DNA. Metal-Bound S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6m | ||||||
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Title | Conjugative Relaxase Trwc In Complex With Orit DNA. Metal-Bound Structure | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / protein-dna complex / bacterial conjugation / relaxase / dna replication / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Guasch, A. / Lucas, M. / Moncalian, G. / Cabezas, M. / Perez-Luque, R. / Gomis-Ruth, F.X. / de la Cruz, F. / Coll, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. Authors: Boer, R. / Russi, S. / Guasch, A. / Lucas, M. / Blanco, A.G. / Perez-Luque, R. / Coll, M. / de la Cruz, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6m.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6m.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1s6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6m ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6m | HTTPS FTP |
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-Related structure data
Related structure data | 1zm5C 2cdmC 1omhS 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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-Components
#1: DNA chain | Mass: 7714.970 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 33082.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q47673 |
#3: Chemical | ChemComp-NI / |
#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: 3.18 Å3/Da / Density % sol: 61.28 % |
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Crystal grow | Temperature: 296 K / pH: 4.6 Details: 25% PEGMM 2000, 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K Temp details: K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.983994 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983994 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→45.264 Å / Num. all: 24644 / Num. obs: 24598 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1omh Resolution: 2.28→43.85 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.28→43.85 Å
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Refine LS restraints |
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