+Open data
-Basic information
Entry | Database: PDB / ID: 1sn7 | ||||||
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Title | KUMAMOLISIN-AS, APOENZYME | ||||||
Components | kumamolisin-As | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information tripeptidyl-peptidase activity / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Alicyclobacillus sendaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wlodawer, A. / Li, M. / Gustchina, A. / Oda, K. / Nishino, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystallographic and biochemical investigations of kumamolisin-as, a serine-carboxyl peptidase with collagenase activity. Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sn7.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sn7.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sn7_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 1sn7_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 1sn7_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1sn7_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/1sn7 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/1sn7 | HTTPS FTP |
-Related structure data
Related structure data | 1sioC 1siuC 1gt9S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 36718.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria) Strain: NTAP-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GB88 |
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#2: Chemical | ChemComp-CA / |
#3: 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: 1.46 Å3/Da / Density % sol: 15.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG8000, Ammounium Sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17755 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rsym value: 0.035 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.125 / % possible all: 61.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1GT9 Resolution: 2→10 Å / Num. parameters: 11263 / Num. restraintsaints: 10565 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2811.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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