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Yorodumi- PDB-5vfx: Structure of an accessory protein of the pCW3 relaxosome in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vfx | ||||||
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Title | Structure of an accessory protein of the pCW3 relaxosome in complex with the origin of transfer (oriT) DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / conjugation / winged helix-turn-helix / oriT / clostridium perfringens / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Cch helix turn helix domain / DNA / DNA (> 10) / Uncharacterized protein Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Traore, D.A.K. / Wisniewski, J.A. / Flanigan, S.F. / Conroy, P.J. / Panjikar, S. / Mok, Y.-F. / Lao, C. / Griffin, M.D.W. / Adams, V. / Rood, J.I. / Whisstock, J.C. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3. Authors: Traore, D.A.K. / Wisniewski, J.A. / Flanigan, S.F. / Conroy, P.J. / Panjikar, S. / Mok, Y.F. / Lao, C. / Griffin, M.D.W. / Adams, V. / Rood, J.I. / Whisstock, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vfx.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vfx.ent.gz | 209.2 KB | Display | PDB format |
PDBx/mmJSON format | 5vfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vfx_validation.pdf.gz | 502.9 KB | Display | wwPDB validaton report |
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Full document | 5vfx_full_validation.pdf.gz | 508.4 KB | Display | |
Data in XML | 5vfx_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5vfx_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vfx ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vfx | HTTPS FTP |
-Related structure data
Related structure data | 5vfySC S: Starting model for refinement 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: 13005.041 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) Gene: ERS852446_03033, pBeta2_00022, pCpb2-CP1_20, pCW3_0028, pNetB-NE10_20, pNetB_00021, pTet_021 Plasmid: pGL12 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q1PLI2 #2: DNA chain | Mass: 7112.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Clostridium perfringens (bacteria) #3: DNA chain | Mass: 7005.545 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Clostridium perfringens (bacteria) #4: 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: 2.92 Å3/Da / Density % sol: 57.84 % / Mosaicity: 0.24 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M imidazole, 50% (v/v) 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.81→47.2 Å / Num. obs: 44405 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 81.15 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.098 / Rrim(I) all: 0.192 / Net I/σ(I): 6.5 / Num. measured all: 166112 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VFY Resolution: 2.81→43.08 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.867 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.313
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Displacement parameters | Biso max: 151.84 Å2 / Biso mean: 67.63 Å2 / Biso min: 23.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→43.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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