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Yorodumi- PDB-4cfz: SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cfz | ||||||
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Title | SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTION AND POWDER DIFFRACTION ANALYSIS | ||||||
Components | SUBTILISIN SAVINASE | ||||||
Keywords | HYDROLASE / SINGLE CRYSTAL ANALYSIS / POWDER DIFFRACTION / QUALITY CONTROL / MICROCRYSTALLINE SUSPENSION | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS LENTUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Frankaer, C.G. / Moroz, O.V. / Turkenburg, J.P. / Aspmo, S.I. / Thymark, M. / Friis, E.P. / Stahla, K. / Nielsen, J.E. / Wilson, K.S. / Harris, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Analysis of an Industrial Production Suspension of Bacillus Lentus Subtilisin Crystals by Powder Diffraction: A Powerful Quality-Control Tool. Authors: Frankaer, C.G. / Moroz, O.V. / Turkenburg, J.P. / Aspmo, S.I. / Thymark, M. / Friis, E.P. / Stahl, K. / Nielsen, J.E. / Wilson, K.S. / Harris, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cfz.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfz.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfz ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfz | HTTPS FTP |
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-Related structure data
Related structure data | 4cfyC 4cg0C 1svnS 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: 26718.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS LENTUS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: P29600, subtilisin | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 33.8 % / Description: NONE |
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Crystal grow | Details: CRYSTALS FROM INDUSTRIAL PRODUCTION SUSPENSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→23.94 Å / Num. obs: 28009 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SVN Resolution: 1.57→23.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.581 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.861 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→23.94 Å
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Refine LS restraints |
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