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Yorodumi- PDB-2zj6: Crystal structure of D337A mutant of Pseudomonas sp. MIS38 lipase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zj6 | ||||||
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Title | Crystal structure of D337A mutant of Pseudomonas sp. MIS38 lipase | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / Family i.3 lipase / Beta roll / Calcium binding protein / RTX protein / Calcium site mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Angkawidjaja, C. / Kuwahara, K. / Kanaya, S. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2008 Title: Importance of the Ca2+-binding sites in the N-catalytic domain of a family I.3 lipase for activity and stability Authors: Kuwahara, K. / Angkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zj6.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zj6.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zj6 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zj6 | HTTPS FTP |
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-Related structure data
Related structure data | 2zj7C 2z8xS 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
#1: Protein | Mass: 64519.848 Da / Num. of mol.: 1 / Mutation: D337A Source method: isolated from a genetically manipulated source Details: Secretory overproduction by co-expression with plasmid pYBCD20 Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: MIS38 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9RBY1, triacylglycerol lipase | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 12, 2007 / Details: mirrors |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→86.39 Å / Num. all: 33670 / Num. obs: 32025 / Redundancy: 5.2 % / Rmerge(I) obs: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8X Resolution: 2.25→39.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.286 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.2 / 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: 19.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.253→2.312 Å / Total num. of bins used: 20
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