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Yorodumi- PDB-2jlh: Crystal Structure of the Cytoplasmic domain of Yersinia Pestis Ys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jlh | ||||||
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Title | Crystal Structure of the Cytoplasmic domain of Yersinia Pestis YscU N263A mutant | ||||||
Components | YOP PROTEINS TRANSLOCATION PROTEIN U | ||||||
Keywords | PROTEIN TRANSPORT / CELL MEMBRANE / TRANSMEMBRANE / YERSINIA PESTIS / MOLECULAR SWITCH / ATOMIC RESOLUTION / MEMBRANE / VIRULENCE / TRANSPORT / TYPE III SECRETION SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | YERSINIA PESTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Lountos, G.T. / Austin, B.P. / Nallamsetty, S. / Waugh, D.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Atomic Resolution Structure of the Cytoplasmic Domain of Yersinia Pestis Yscu, a Regulatory Switch Involved in Type III Secretion. Authors: Lountos, G.T. / Austin, B.P. / Nallamsetty, S. / 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 | 2jlh.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jlh.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jlh_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 2jlh_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 2jlh_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2jlh_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlh ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlh | HTTPS FTP |
-Related structure data
Related structure data | 2jliC 2jljSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16907.504 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 211-354 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PBA2086 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P69986 | ||||
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#2: Chemical | ChemComp-1PE / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.5 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100 MM HEPES PH 7.5, 1 M SODIUM MALONATE PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97921 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 22446 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 63.4 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.2 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JLJ Resolution: 1.53→46.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.51 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→46.88 Å
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Refine LS restraints |
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