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Yorodumi- PDB-2yjl: Structural characterization of a secretin pilot protein from the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yjl | ||||||
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Title | Structural characterization of a secretin pilot protein from the type III secretion system (T3SS) of Pseudomonas aeruginosa | ||||||
Components | EXOENZYME S SYNTHESIS PROTEIN B | ||||||
Keywords | LIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / PILOTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å | ||||||
Authors | Izore, T. / Perdu, C. / Job, V. / Atree, I. / Faudry, E. / Dessen, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural Characterization and Membrane Localization of Exsb from the Type III Secretion System (T3Ss) of Pseudomonas Aeruginosa Authors: Izore, T. / Perdu, C. / Job, V. / Atree, I. / Faudry, E. / Dessen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yjl.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yjl.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yjl_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 2yjl_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 2yjl_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 2yjl_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjl ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 13817.702 Da / Num. of mol.: 3 / Fragment: RESIDUES 13-137 Source method: isolated from a genetically manipulated source Details: SEQUENCE ENCOMPASSES RESIDUES 17-141 OF NATIVELY-EXPRESSED FULL-LENGTH PROTEIN Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA II / References: UniProt: P26994 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | Sequence details | AN ALTERNATIVE START CODON WAS IDENTIFIED IN THIS STUDY, ADDING 4 AMINO TERMINAL RESIDUES TO THE ...AN ALTERNATIV | |
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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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: TRIS 0.1 M PH 8.5, AMMONIUM SULFATE 1.5 M, GLYCEROL 10%. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→35 Å / Num. obs: 35870 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 28.825 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.81→1.92 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 75.6 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.81→35.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.679 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154 / 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: 31.183 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→35.54 Å
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Refine LS restraints |
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