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Yorodumi- PDB-1ga6: CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ga6 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL PROTEINASE) COMPLEXED WITH A FRAGMENT OF TYROSTATIN (THIS ENZYME RENAMED "SEDOLISIN" IN 2003) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE-CARBOXYL PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information sedolisin / tripeptidyl-peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1GA1 / Resolution: 1 Å | ||||||
Authors | Wlodawer, A. / Li, M. / Dauter, Z. / Gustchina, A. / Uchida, K. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes. Authors: Wlodawer, A. / Li, M. / Dauter, Z. / Gustchina, A. / Uchida, K. / Oyama, H. / Dunn, B.M. / Oda, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ga6.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ga6.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 1ga6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ga6_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 1ga6_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 1ga6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1ga6_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1ga6 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1ga6 | HTTPS FTP |
-Related structure data
Related structure data | 1ga4C 1ga1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AI
#1: Protein | Mass: 38446.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Plasmid: PUKCP2212 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P42790, EC: 3.4.23.37 |
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#2: Protein/peptide | Mass: 351.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The inhibitor was chemically synthesized. |
-Non-polymers , 4 types, 475 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Details
Compound details | TYROSTATIN IS A NATURAL INHIBITOR, COMPOSED OF ISOVALERYL-TYROSYL-LEUSYL-TYROSINAL. IN 1GA1 AND ...TYROSTATIN |
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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: 2.94 Å3/Da / Density % sol: 58.17 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 5% guanidine, 7% glycerol, 5% methanol, 1.0 M ammonium sulfate, 0.1 M sodium citrate buffer pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.8 | |||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2000 / Details: focussing mirror |
Radiation | Monochromator: Si(111) double crystal, sagitally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1→10 Å / Num. all: 241182 / Num. obs: 202008 / % possible obs: 84 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 6.58 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.7 / Num. unique all: 24057 / % possible all: 10 |
Reflection | *PLUS Num. measured all: 2554920 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH 1GA1 Starting model: PDB ENTRY 1GA1 Resolution: 1→10 Å / Cross valid method: R-FREE / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: Anisotropic refinement of individual atoms. Parameter errors estimated from least-squares blocked full-matrix inversion.
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Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→10 Å
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