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Yorodumi- PDB-1omh: Conjugative Relaxase TrwC in complex with OriT Dna. Metal-free st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1omh | ||||||
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Title | Conjugative Relaxase TrwC in complex with OriT Dna. Metal-free structure. | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / BACTERIAL CONJUGATION / RELAXASE / DNA REPLICATION / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information G-quadruplex DNA unwinding / mitochondrial genome maintenance / replication fork reversal / telomere maintenance / single-stranded DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 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: Nat.Struct.Biol. / Year: 2003 Title: Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Authors: Guasch, A. / Lucas, M. / Moncalian, G. / Cabezas, M. / Perez-Luque, R. / Gomis-Ruth, F.X. / de la Cruz, F. / Coll, M. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Two active-site tyrosyl residues of protein TrwC act sequentially at the origin of transfer during plasmid R388 conjugation Authors: Grandoso, G. / Avila, P. / Cayon, A. / Hernando, M.A. / Llosa, M. / de la Cruz, F. #2: Journal: MOL.MICROBIOL. / Year: 2002 Title: Bacterial conjugation: a two-step mechanism for DNA transport. Authors: Llosa, M. / Gomis-Ruth, F.X. / 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 | 1omh.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1omh.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1omh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/1omh ftp://data.pdbj.org/pub/pdb/validation_reports/om/1omh | HTTPS FTP |
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-Related 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 / Details: DNA FORMING A CRUCIFORM ARM | ||
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#2: Protein | Mass: 33082.414 Da / Num. of mol.: 1 / Fragment: N-terminal relaxase domain 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 | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / 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 | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002 | |||||||||||||||
Radiation | Monochromator: diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→50 Å / Num. obs: 64999 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.146 | |||||||||||||||
Reflection shell | Resolution: 1.95→50 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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