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Yorodumi- PDB-3sze: Crystal structure of the passenger domain of the E. coli autotran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sze | ||||||
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Title | Crystal structure of the passenger domain of the E. coli autotransporter EspP | ||||||
Components | Serine protease espP | ||||||
Keywords | HYDROLASE / parallel beta-helix / serine protease | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Khan, S. / Mian, H.S. / Sandercock, L.E. / Battaile, K.P. / Lam, R. / Chirgadze, N.Y. / Pai, E.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structure of the Passenger Domain of the Escherichia coli Autotransporter EspP. Authors: Khan, S. / Mian, H.S. / Sandercock, L.E. / Chirgadze, N.Y. / Pai, E.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sze.cif.gz | 373.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sze.ent.gz | 302.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3sze ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3sze | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 105535.258 Da / Num. of mol.: 1 / Fragment: passenger domain, UNP residues 56-1023 / Mutation: S263A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: EDL933 / Gene: ECO57PM78, espP, L7020 / Plasmid: pB9-5-S263A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q7BSW5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: 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: 2.88 Å3/Da / Density % sol: 57.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18 22% PEG 4000, 0.1M HEPES, 0.05 0.15M tri-lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2007 |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→85.13 Å / Num. all: 43770 / Num. obs: 43730 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.99 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.86 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.943 / SU ML: 0.178 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 13.99 / ESU R Free: 0.252 / 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: 32.213 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 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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