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Yorodumi- PDB-4p0y: Structure of the double stranded DNA binding type IV secretion pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p0y | ||||||
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Title | Structure of the double stranded DNA binding type IV secretion protein TraN from Enterococcus | ||||||
Components | AM32 | ||||||
Keywords | DNA BINDING PROTEIN / GRAM-POSITIVE / CONJUGATION / HELIX-TURN-HELIX / DSDNA BINDING | ||||||
Function / homology | isomerase activity / AM32 Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Goessweiner-mohr, N. / Fercher, C. / Keller, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the double-stranded DNA-binding type IV secretion protein TraN from Enterococcus. Authors: Goessweiner-Mohr, N. / Eder, M. / Hofer, G. / Fercher, C. / Arends, K. / Birner-Gruenberger, R. / Grohmann, E. / Keller, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p0y.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p0y.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 4p0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/4p0y ftp://data.pdbj.org/pub/pdb/validation_reports/p0/4p0y | HTTPS FTP |
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-Related structure data
Related structure data | 4p0zC 4pm3C 4edc 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17787.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: PQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7BVV5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: BIS-TRIS, PEG 3.350, PH 5.5, MICROBATCH UNDER OIL, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010 Details: TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION DEMAGNIFICATION) |
Radiation | Monochromator: BARTELS MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→55.87 Å / Num. obs: 43358 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.085 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1 / Rsym value: 0.776 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→21.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.189 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→21.35 Å
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Refine LS restraints |
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