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Yorodumi- PDB-4fmp: Crystal structure of thermostable, organic-solvent tolerant lipas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fmp | ||||||
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Title | Crystal structure of thermostable, organic-solvent tolerant lipase from Geobacillus sp. strain ARM | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold / Alpha/beta fold | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nisbar, N.D. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Leow, A.T.C. | ||||||
Citation | Journal: Thesis / Year: 2013 Title: Crystallization of novel ARM lipase and elucidation of its space-grown crystal structure Authors: Nisbar, N.D. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Leow, A.T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fmp.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fmp.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/4fmp ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmp | HTTPS FTP |
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-Related structure data
Related structure data | 2dsnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42551.480 Da / Num. of mol.: 2 / Fragment: unp residues 35-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: ARM / Plasmid: pTrcHis2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93A71, triacylglycerol lipase #2: Chemical | #3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 0.1M MES monohydrate, 12% v/v PEG 20000, pH 6.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2011 |
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 42814 / Num. obs: 42814 / % possible obs: 98 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2DSN Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.787 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.225 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.167 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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