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Yorodumi- PDB-1nlu: Pseudomonas sedolisin (serine-carboxyl proteinase) complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nlu | ||||||
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Title | Pseudomonas sedolisin (serine-carboxyl proteinase) complexed with two molecules of pseudo-iodotyrostatin | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PSCP / 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 / AB INITIO / Resolution: 1.3 Å | ||||||
Authors | Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Glodfarb, N.E. / Dunn, B.M. / Oda, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Two inhibitor molecules bound in the active site of Pseudomonas sedolisin: a model for the bi-product complex following cleavage of a peptide substrate. Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Oyama, H. / Oda, K. / Beyer, B.B. / Clemente, J. / Dunn, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nlu.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nlu.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nlu ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nlu | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 38250.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: PCP / Production host: Escherichia coli (E. coli) / References: UniProt: P42790, sedolisin | ||||
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#2: Protein/peptide | #3: Chemical | ChemComp-CA / | #4: 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: 2.22 Å3/Da / Density % sol: 57.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.8 / Method: unknown / Details: Wlodawer, A., (2001) Biochemistry, 40, 15602. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 9, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 110018 / Num. obs: 110018 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rsym value: 0.082 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.3→1.35 Å / Mean I/σ(I) obs: 2.28 / Num. unique all: 10917 / Rsym value: 0.77 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 848476 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.3→10 Å / Num. parameters: 28486 / Num. restraintsaints: 34716 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3137 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.3 Å / Rfactor Rfree: 0.1944 / Rfactor Rwork: 0.1637 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |