+Open data
-Basic information
Entry | Database: PDB / ID: 3bzy | ||||||
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Title | Crystal structure of the mutated Y316D EscU C-terminal domain | ||||||
Components | (EscURecea-Cristur) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / flagella / Intein / T3SS / membrane | ||||||
Function / homology | Function and homology information dioxygenase activity / protein secretion / isomerase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | ||||||
Authors | Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS. Authors: Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / 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 | 3bzy.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bzy.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/3bzy ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bzy | HTTPS FTP |
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-Related structure data
Related structure data | 3bzlC 3bzoC 3bzpC 3bzrC 3bzsC 3bztC 3bzvC 3bzxC 3bzzC 3c00C 3c01C 3c03C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 5991.751 Da / Num. of mol.: 1 / Fragment: UNP residues 215-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26 |
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#2: Protein | Mass: 9431.979 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: Y316D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26 |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 1.92 Å3/Da / Density % sol: 36.05 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.5 Details: Li2SO4, Bis-Tris, Peg3350, NaCl, pH 5.5, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2007 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. all: 37475 / Num. obs: 36351 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.3 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.2→45.6 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.957 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.038 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.423 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→45.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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