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Yorodumi- PDB-4lvi: MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT... -
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-Basic information
Entry | Database: PDB / ID: 4lvi | ||||||
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Title | MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 4.6 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Protein-DNA complex / Pfam Family: Mob_Pre (PF01076). MOBv Family of Relaxases / relaxase/endonuclease / oriT DNA / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Pluta, R. / Boer, D.R. / Coll, M. | ||||||
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 | 4lvi.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lvi.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lvi_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 4lvi_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 4lvi_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4lvi_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/4lvi ftp://data.pdbj.org/pub/pdb/validation_reports/lv/4lvi | 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 , 1 types, 1 molecules A
#1: Protein | Mass: 23168.918 Da / Num. of mol.: 1 / Fragment: Relaxase Domain of MobM protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: pre, mob / Plasmid: pQE-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P13925 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 2087.409 Da / Num. of mol.: 1 Fragment: oligonucleotide_1 mimicking pMV158 oriT DNA hairpin Source method: obtained synthetically Details: Oligonucleotides were obtained from Biomers (Ulm, Germany). |
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#3: DNA chain | Mass: 4672.070 Da / Num. of mol.: 1 Fragment: oligonucleotide_2 mimicking pMV158 oriT DNA hairpin Source method: obtained synthetically Details: Oligonucleotides were obtained from Biomers (Ulm, Germany). |
-Non-polymers , 3 types, 136 molecules
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-GOL / |
#6: 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: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 20-22% PEG 6000, 0.1M Sodium Acetate, pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 |
Radiation | Monochromator: channel cut ESRF monochromator Crystal Type Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.1 Å / Num. obs: 25154 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Resolution: 1.9→48.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.641 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 48.481 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.1 Å
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