+Open data
-Basic information
Entry | Database: PDB / ID: 3utk | ||||||
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Title | Structure of the pilotin of the type II secretion system | ||||||
Components | Lipoprotein outS | ||||||
Keywords | PROTEIN TRANSPORT / Nested (perpendicular) alpha-helical hairpins / PILOT PROTEIN | ||||||
Function / homology | Function and homology information cell outer membrane / intracellular protein transport / protein processing Similarity search - Function | ||||||
Biological species | Dickeya dadantii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Rehman, S. / Pickersgill, R.W. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of the pilotin of the type II secretion system Authors: Gu, S. / Rehman, S. / Wang, X. / Shevchik, V.E. / Pickersgill, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3utk.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3utk.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 3utk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/3utk ftp://data.pdbj.org/pub/pdb/validation_reports/ut/3utk | HTTPS FTP |
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-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: 14349.450 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: outS, Dda3937_02411 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q01567 #2: 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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M ammonium sulfate, 2% PEG 400, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0718 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2010 / Details: Silicon monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.78 Å / Num. all: 32767 / Num. obs: 32440 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.2 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4652 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→46.762 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.19 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→46.762 Å
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Refine LS restraints |
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LS refinement shell |
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