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Yorodumi- PDB-1i78: CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i78 | ||||||
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Title | CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHIA COLI | ||||||
Components | PROTEASE VII | ||||||
Keywords | HYDROLASE / integral outer membrane protein / protease / beta barrel | ||||||
Function / homology | Function and homology information omptin / : / cell outer membrane / endopeptidase activity / aspartic-type endopeptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Vandeputte-Rutten, L. / Kramer, R.A. / Kroon, J. / Dekker, N. / Egmond, M.R. / Gros, P. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site. Authors: Vandeputte-Rutten, L. / Kramer, R.A. / Kroon, J. / Dekker, N. / Egmond, M.R. / Gros, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i78.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i78.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i78_validation.pdf.gz | 938.7 KB | Display | wwPDB validaton report |
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Full document | 1i78_full_validation.pdf.gz | 963.9 KB | Display | |
Data in XML | 1i78_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 1i78_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i78 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i78 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | OmpT is active as a monomer. The assymetric unit contains two monomers. |
-Components
#1: Protein | Mass: 33495.594 Da / Num. of mol.: 2 / Mutation: S99A,G216K,K217G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: OMPT / Plasmid: PRAK11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09169, EC: 3.4.21.87 #2: Sugar | ChemComp-BOG / #3: Chemical | #4: 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: 3.45 Å3/Da / Density % sol: 64.4 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% (v/v) 2-methyl-2,4-pentanediol, 0.3 M sodium citrate PH 5.5, 1% (w/v) octyl-beta-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9322 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 1999 / Details: toroidal mirror |
Radiation | Monochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 29075 / Num. obs: 27400 / % possible obs: 94.3 % / Redundancy: 1.59 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.82 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.54 / Num. unique all: 2766 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 43471 |
Reflection shell | *PLUS Lowest resolution: 2.69 Å / % possible obs: 97.7 % / Num. unique obs: 2766 / Num. measured obs: 4352 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.238 / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 53 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.318 |