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Yorodumi- PDB-6ejp: Yersinia YscU C-terminal fragment in complex with a synthetic compound -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ejp | ||||||
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Title | Yersinia YscU C-terminal fragment in complex with a synthetic compound | ||||||
Components | (Yop proteins translocation protein ...) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / AUTOCLEAVAGE / TYPE III SECRETION SYSTEM / INHIBITOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Ho, O. / Sunduru, N. / Elofsson, M. / Wolf-Watz, M. / Schuler, H. | ||||||
Citation | Journal: To Be Published Title: Yersinia YscU C-terminal fragment in complex with a synthetic compound Authors: Karlberg, T. / Thorsell, A.G. / Ho, O. / Sunduru, N. / Elofsson, M. / Wolf-Watz, M. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ejp.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ejp.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ejp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6ejp ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ejp | HTTPS FTP |
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-Related structure data
Related structure data | 2jliS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Yop proteins translocation protein ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 6832.867 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, UNP residues 211-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscU, YPCD1.47, y5031, y0034, YP_pCD36 / Plasmid: PGEX / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / References: UniProt: P69986 #2: Protein | Mass: 10547.121 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 264-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscU, YPCD1.47, y5031, y0034, YP_pCD36 / Plasmid: PGEX / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / References: UniProt: P69986 |
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-Non-polymers , 5 types, 23 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: 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: 3.27 Å3/Da / Density % sol: 62.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.8 M potassium dihydrogen phosphate, 0.8 M disodium hydrogen phosphate, 0.1 M Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→44.8 Å / Num. obs: 16706 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 68.39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.48→2.63 Å / Redundancy: 14 % / Rmerge(I) obs: 0.877 / Num. unique obs: 2613 / CC1/2: 0.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JLI Resolution: 2.48→23.39 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.8956 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.237
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Displacement parameters | Biso mean: 68.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.385 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.48→23.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.48→2.65 Å / Total num. of bins used: 8
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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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