+Open data
-Basic information
Entry | Database: PDB / ID: 1xl3 | ||||||
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Title | Complex structure of Y.pestis virulence Factors YopN and TyeA | ||||||
Components |
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Keywords | CELL INVASION / yopN / TyeA / Yersinia pestis / type III secretion | ||||||
Function / homology | Function and homology information protein secretion by the type III secretion system / negative regulation of protein secretion / cell outer membrane / cell surface Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schubot, F.D. / Jackson, M.W. / Penrose, K.J. / Cherry, S. / Tropea, J.E. / Plano, G.V. / Waugh, D.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis. Authors: Schubot, F.D. / Jackson, M.W. / Penrose, K.J. / Cherry, S. / Tropea, J.E. / Plano, G.V. / Waugh, D.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB Authors: Schubot, F.D. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xl3.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xl3.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xl3_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 1xl3_full_validation.pdf.gz | 487.7 KB | Display | |
Data in XML | 1xl3_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1xl3_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/1xl3 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/1xl3 | HTTPS FTP |
-Related structure data
Related structure data | 1xkpSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
#1: Protein | Mass: 24642.873 Da / Num. of mol.: 2 / Mutation: residues 76-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yopN, lcrE / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 3822072, UniProt: P68640*PLUS #2: Protein | Mass: 10844.321 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: tyeA / Plasmid: pDest42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16161, UniProt: P69968*PLUS #3: 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: 2.75 Å3/Da / Density % sol: 55.21 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 40229 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XKP chain A residues 76-269 Resolution: 2.2→84.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.207 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / ESU R: 0.236 / ESU R Free: 0.21 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→84.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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