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Yorodumi- PDB-5n2q: MobM Relaxase Domain (MOBV; Mob_Pre) bound to 26nt pMV158 oriT DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n2q | ||||||
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Title | MobM Relaxase Domain (MOBV; Mob_Pre) bound to 26nt pMV158 oriT DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / relaxase / nuclease / conjugation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) Plasmid pMV158 (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Russi, S. / Boer, D.R. / Coll, M. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. Authors: Pluta, R. / Boer, D.R. / Lorenzo-Diaz, F. / Russi, S. / Gomez, H. / Fernandez-Lopez, C. / Perez-Luque, R. / Orozco, M. / Espinosa, M. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n2q.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n2q.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 5n2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n2q_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 5n2q_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 5n2q_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 5n2q_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/5n2q ftp://data.pdbj.org/pub/pdb/validation_reports/n2/5n2q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 23590.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: pre, mob / Production host: Escherichia coli (E. coli) / References: UniProt: P13925 |
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#2: DNA chain | Mass: 8377.456 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmid pMV158 (others) / Production host: synthetic construct (others) |
-Non-polymers , 5 types, 159 molecules
#3: Chemical | ChemComp-CL / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-NA / |
#7: 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: 1.96 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 4.6 / Details: 100 mM NaAc, pH 4.6 and 10% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.73 Å / Num. obs: 16179 / % possible obs: 98.6 % / Redundancy: 4.1 % / Net I/σ(I): 10.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→55.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.546 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.183 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.718 Å2
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Refinement step | Cycle: 1 / Resolution: 2→55.73 Å
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