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Yorodumi- PDB-4cg0: Savinase crystal structures for combined single crystal diffracti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cg0 | ||||||
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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: 1.36 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 | 4cg0.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cg0.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 4cg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/4cg0 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/4cg0 | HTTPS FTP |
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-Related structure data
Related structure data | 4cfyC 4cfzC 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.7 % / 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: I03 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→17.8 Å / Num. obs: 46289 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.36→1.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SVN Resolution: 1.36→44.8 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.055 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / 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: 15.461 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→44.8 Å
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Refine LS restraints |
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