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Yorodumi- PDB-1kap: THREE-DIMENSIONAL STRUCTURE OF THE ALKALINE PROTEASE OF PSEUDOMON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kap | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THE ALKALINE PROTEASE OF PSEUDOMONAS AERUGINOSA: A TWO-DOMAIN PROTEIN WITH A CALCIUM BINDING PARALLEL BETA ROLL MOTIF | ||||||
Components |
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Keywords | ZINC METALLOPROTEASE / CALCIUM BINDING PROTEIN | ||||||
Function / homology | Function and homology information serralysin / negative regulation of complement activation, lectin pathway / negative regulation of complement activation, classical pathway / positive regulation of sodium ion transport / metalloendopeptidase activity / peptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.64 Å | ||||||
Authors | Baumann, U. / Wu, S. / Flaherty, K.M. / Mckay, D.B. | ||||||
Citation | Journal: EMBO J. / Year: 1993 Title: Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. Authors: Baumann, U. / Wu, S. / Flaherty, K.M. / McKay, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kap.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kap.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kap_validation.pdf.gz | 367.8 KB | Display | wwPDB validaton report |
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Full document | 1kap_full_validation.pdf.gz | 368.5 KB | Display | |
Data in XML | 1kap_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1kap_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kap ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kap | 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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Unit cell |
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-Components
#1: Protein | Mass: 50464.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 References: UniProt: Q03023, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||
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#2: Protein/peptide | Mass: 363.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-CA / #5: 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: 3.15 Å3/Da / Density % sol: 60.92 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: unknown / PH range low: 5 / PH range high: 4.6 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
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Detector | Type: MARRESEARCH / Date: Feb 22, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→25 Å / Num. obs: 75163 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Resolution: 1.64→10 Å / σ(F): 2 Details: IN THE LATER STAGES OF MODEL BUILDING AND REFINEMENT, IT BECAME APPARENT THAT THERE WAS "EXTRA" ELECTRON DENSITY IN THE ACTIVE SITE CLEFT OF THE PROTEOLYTIC DOMAIN. IT HAS PROVED POSSIBLE TO ...Details: IN THE LATER STAGES OF MODEL BUILDING AND REFINEMENT, IT BECAME APPARENT THAT THERE WAS "EXTRA" ELECTRON DENSITY IN THE ACTIVE SITE CLEFT OF THE PROTEOLYTIC DOMAIN. IT HAS PROVED POSSIBLE TO RELIABLY MODEL THE BACKBONE OF A TETRAPEPTIDE INTO THI DENSITY. DENSITIES FOR SIDE CHAINS ARE ALSO APPARENT; HOWEVER, THEY DO NOT REVEAL A UNIQUE SEQUENCE, AND THE AUTHORS PRESUME THAT THE BOUND PEPTIDE IS HOMOLOGOUS IN SEQUENCE. THE AUTHORS ASSUME THAT THIS PEPTIDE IS A PRODUCT OF HYDROLYSIS.
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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