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Yorodumi- PDB-6o1x: Structure of pCW3 conjugation coupling protein TcpA monomer form ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o1x | |||||||||
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Title | Structure of pCW3 conjugation coupling protein TcpA monomer form with ATPgS | |||||||||
Components | DNA translocase coupling protein | |||||||||
Keywords | TRANSLOCASE / ATPase / Conjugation | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å | |||||||||
Authors | Traore, D.A.K. / Ahktar, N. / Torres, V.T. / Adams, V. / Coulibaly, F. / Panjikar, S. / Caradoc-Davies, T.T. / Rood, J.I. / Whisstock, J.C. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: To be published Title: Structure of pCW3 conjugation coupling protein TcpA Authors: Traore, D.A.K. / 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 | 6o1x.cif.gz | 296.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o1x.ent.gz | 238.2 KB | Display | PDB format |
PDBx/mmJSON format | 6o1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o1x_validation.pdf.gz | 800.6 KB | Display | wwPDB validaton report |
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Full document | 6o1x_full_validation.pdf.gz | 805.1 KB | Display | |
Data in XML | 6o1x_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6o1x_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/6o1x ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o1x | HTTPS FTP |
-Related structure data
Related structure data | 6o1wSC 6o1yC 6o1zC 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: 40435.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: tcpA, pCW3_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PLI0 #2: Sugar | #3: Chemical | ChemComp-AGS / | #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: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20 % (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9737 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.46→48.97 Å / Num. obs: 25446 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 52.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.038 / Rrim(I) all: 0.115 / Net I/σ(I): 13 / Num. measured all: 228939 / Scaling rejects: 23 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6O1W Resolution: 2.46→46.2 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.835 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.275
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Displacement parameters | Biso max: 134.42 Å2 / Biso mean: 55.59 Å2 / Biso min: 15.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.46→46.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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