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- PDB-2cdm: The structure of TrwC complexed with a 27-mer DNA comprising the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cdm | ||||||
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Title | The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site | ||||||
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![]() | DNA/DNA-BINDING PROTEIN / RELAXASE / BACTERIAL CONJUGATION / DNA TRANSFER / DNA-PROTEIN COMPLEX / DNA-DNA-BINDING PROTEIN complex | ||||||
Function / homology | ![]() G-quadruplex DNA unwinding / mitochondrial genome maintenance / replication fork reversal / telomere maintenance / single-stranded DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boer, R. / Russi, S. / Guasch, A. / Lucas, M. / Blanco, A.G. / Perez-Luque, R. / Coll, M. / de la Cruz, F. | ||||||
![]() | ![]() 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. #1: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s6mC ![]() 1zm5C ![]() 1osbS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33066.414 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-293 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SELENO METHIONINE DERIVATIVE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 8332.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: FROM THE PLASMID R388 / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUES 1-293 T27 DISORDERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | pH: 4.6 Details: 32 % PEG MME 2000, 0.3 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 26, 2004 / Details: CRYSTALS AND MIRRORS |
Radiation | Monochromator: DIAMOND CRYSTAL (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979269 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 27451 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OSB Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.49 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.72 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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