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Yorodumi- PDB-6m8y: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m8y | ||||||||||||
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Title | PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF | ||||||||||||
Components |
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Keywords | Hydrolase/Hydrolase inhibitor / Serine-carboxyl proteinase / Hydrolase-hydrolase inhibitor complex | ||||||||||||
Function / homology | Function and homology information sedolisin / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas sp. (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å | ||||||||||||
Authors | Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / Dunn, B.M. / Oda, K. | ||||||||||||
Funding support | Japan, United States, 3items
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Citation | Journal: Biochemistry / Year: 2001 Title: Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / 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 | 6m8y.cif.gz | 224.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m8y.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/6m8y ftp://data.pdbj.org/pub/pdb/validation_reports/m8/6m8y | HTTPS FTP |
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-Related structure data
Related structure data | 6m8wC 6m9cC 6m9dC 6m9fC 1ga6S 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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Details | As per the authors the biological assembly is a monomer |
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 38179.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (strain 101) (bacteria) Strain: 101 / Gene: pcp / Production host: Escherichia coli (E. coli) / References: UniProt: P42790, sedolisin |
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#2: Protein/peptide | |
-Non-polymers , 4 types, 453 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | THE UNBOUND INHIBITOR (CHAIN B) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L-PHENYLALANINE ...THE UNBOUND INHIBITOR (CHAIN B) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L-PHENYLALAN |
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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: 2.95 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium sulfate, glycerol, guanidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2001 / Details: Mirrors |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→40 Å / Num. obs: 181161 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Χ2: 1.038 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.474 / Num. unique obs: 18060 / Χ2: 0.987 / % possible all: 100 |
-Processing
Software |
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Refinement | Starting model: 1GA6 Resolution: 1.1→30 Å / Num. constraints: 35937 / Num. parameters: 29276 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER Details: THIS ENTRY REPRESENTS RE-REFINEMENT OF THE 1KDY DATA SET USING THE ORIGINAL DIFFRACTION DATA, CORRECTING SOME ERRORS FOUND IN THE ORIGINAL DEPOSITION
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Displacement parameters | Biso max: 131.85 Å2 / Biso mean: 15.2411 Å2 / Biso min: 5.27 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→30 Å
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Refine LS restraints |
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