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Yorodumi- PDB-4hic: Crystal structure of the potential transfer protein TraK from Gra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hic | ||||||
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Title | Crystal structure of the potential transfer protein TraK from Gram-positive conjugative plasmid pIP501 | ||||||
Components | TraK | ||||||
Keywords | UNKNOWN FUNCTION / Gram-positive / type-IV secretion / pIP501 / anti-parallel beta-sheets | ||||||
Function / homology | membrane => GO:0016020 / Uncharacterized protein Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å | ||||||
Authors | Goessweiner-Mohr, N. / Keller, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The type IV secretion protein TraK from the Enterococcus conjugative plasmid pIP501 exhibits a novel fold Authors: Goessweiner-Mohr, N. / Fercher, C. / Arends, K. / Birner-Gruenberger, R. / Laverde-Gomez, D. / Huebner, J. / 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 | 4hic.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hic.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hic_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 4hic_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 4hic_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 4hic_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/4hic ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hic | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30643.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: ORF11 from conjugative plasmid pIP501 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8L1C9 |
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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: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion: microbatch under oil / pH: 6.5 Details: 1:1 setup of purification buffer with Morpheus screen condition 52 (12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, ethylene glycols mix, 0.1 M MES/Imidazol); final protein concentration: 6.45 ...Details: 1:1 setup of purification buffer with Morpheus screen condition 52 (12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, ethylene glycols mix, 0.1 M MES/Imidazol); final protein concentration: 6.45 mg/ml, pH 6.5, vapor diffusion: 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: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2010 Details: toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: BARTELS MONOCROMATOR / Protocol: Native / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,k,-l / Fraction: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.001→82.835 Å / Num. all: 15465 / Num. obs: 15465 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.094 / Net I/σ(I): 12.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.001→40.319 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7381 / σ(F): 0 / Phase error: 33.08 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.11 Å2 / Biso mean: 59.7934 Å2 / Biso min: 32.07 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.001→40.319 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 95 %
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