+Open data
-Basic information
Entry | Database: PDB / ID: 1r8i | ||||||
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Title | Crystal structure of TraC | ||||||
Components | TraC | ||||||
Keywords | STRUCTURAL PROTEIN / TraC / VirB5 / helical bundle | ||||||
Function / homology | Type IV secretion system, VirB5-domain / Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / TraC Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Yeo, H.-J. / Yuan, Q. / Beck, M.R. / Baron, C. / Waksman, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101 Authors: Yeo, H.-J. / Yuan, Q. / Beck, M.R. / Baron, C. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r8i.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r8i.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r8i_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 1r8i_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 1r8i_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1r8i_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r8i ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r8i | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23515.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trac / Plasmid: pTrcTraC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109, DL41 / References: UniProt: Q9L6G5 |
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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: 3.9 Å3/Da / Density % sol: 68.43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: ammonium sulfate, sodium citrate, sodium chloride, glycerol, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. all: 13072 / Num. obs: 13072 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.068 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.3 / % possible all: 92.1 |
Reflection | *PLUS Num. measured all: 106523 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 92.1 % / Rmerge(I) obs: 0.301 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→24.66 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 758670.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7153 Å2 / ksol: 0.2878 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 25 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2883 / Rfactor Rwork: 0.2636 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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