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Yorodumi- PDB-3gr5: Periplasmic domain of the outer membrane secretin EscC from enter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gr5 | ||||||
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Title | Periplasmic domain of the outer membrane secretin EscC from enteropathogenic E.coli (EPEC) | ||||||
Components | EscC | ||||||
Keywords | MEMBRANE PROTEIN / secretin / Type III secretion system / outer membrane / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Yip, C.K. / Vockovic, M. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Authors: Spreter, T. / Yip, C.K. / Sanowar, S. / Andre, I. / Kimbrough, T.G. / Vuckovic, M. / Pfuetzner, R.A. / Deng, W. / Yu, A.C. / Finlay, B.B. / Baker, D. / Miller, S.I. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gr5.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gr5.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/3gr5 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3gr5 | HTTPS FTP |
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-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17857.307 Da / Num. of mol.: 1 / Fragment: EscC periplasmic domain, residues 21-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: escC / Production host: Escherichia coli (E. coli) / References: UniProt: O52135 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.24 % |
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Crystal grow | Details: microbatch, 2.0 M Ammonium sulfate + 0.1 M sodium acetate pH 4.5 or Bis-Tris pH 6.5 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.05→18.7 Å / Num. obs: 20942 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→18.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.57 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.46 Å2 / Biso mean: 42.164 Å2 / Biso min: 19.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→18.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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