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Yorodumi- PDB-3a70: Crystal structure of Pseudomonas sp. MIS38 lipase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a70 | ||||||
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Title | Crystal structure of Pseudomonas sp. MIS38 lipase in complex with diethyl phosphate | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / Family I.3 lipase / beta-roll / open conformation / inhibitor-bound | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas (RNA similarity group I) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Angkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids Authors: 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 | 3a70.cif.gz | 268.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a70.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 3a70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a70 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a70 | HTTPS FTP |
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-Related structure data
Related structure data | 2zvdSC 3a6zC 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
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 64563.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: MIS38 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9RBY1, triacylglycerol lipase |
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-Non-polymers , 5 types, 1149 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, pH8.5, 0.2M ammonium acetaet, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 27, 2009 / Details: mirrors |
Radiation | Monochromator: Rh mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 88120 / % possible obs: 99.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.124 / Rsym value: 0.112 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.44 / Num. unique all: 8629 / Rsym value: 0.376 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZVD Resolution: 2.15→31.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.18 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.171 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 21.854 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→31.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.207 Å / Total num. of bins used: 20
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