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Yorodumi- PDB-7pkw: Crystal structure of VIRB8-like OrfG central and C-terminal domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pkw | ||||||
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Title | Crystal structure of VIRB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system). | ||||||
Components | Putative transfer protein | ||||||
Keywords | TRANSPORT PROTEIN / VirB8-like protein / Type IV secretion system / T4SS | ||||||
Function / homology | Conjugative transposon protein TcpC / TcpC, C-terminal / Conjugative transposon protein TcpC / membrane / Putative transfer protein Function and homology information | ||||||
Biological species | Streptococcus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å | ||||||
Authors | Favier, F. / Didierjean, C. / Cappele, J. / Douzi, B. / Leblond-Bourget, N. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of VIRB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system). Authors: Favier, F. / Didierjean, C. / Cappele, J. / Douzi, B. / Leblond-Bourget, N. #1: Journal: Front Mol Biosci / Year: 2021 Title: Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICE Authors: Cappele, J. / Mohamad Ali, A. / Leblond-Bourget, N. / Mathiot, S. / Dhalleine, T. / Payot, S. / Savko, M. / Didierjean, C. / Favier, F. / Douzi, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pkw.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pkw.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/7pkw ftp://data.pdbj.org/pub/pdb/validation_reports/pk/7pkw | HTTPS FTP |
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-Related structure data
Related structure data | 3ub1S 6zgnS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30884.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Plasmid: PLYSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70CA4 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ammonium sulfate, 1.26 M; cacodylate buffer pH 6.5, 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.835→50 Å / Num. obs: 29698 / % possible obs: 99.8 % / Redundancy: 77.4 % / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 48.17 |
Reflection shell | Resolution: 1.835→1.95 Å / Redundancy: 77 % / Mean I/σ(I) obs: 4.62 / Num. unique obs: 4676 / CC1/2: 0.9448 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6zgn, 3ub1 Resolution: 1.835→44.17 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 31.54 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.835→44.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.835→1.883 Å
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