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Yorodumi- PDB-5xks: Crystal structure of monoacylglycerol lipase from thermophilic Ge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xks | ||||||
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Title | Crystal structure of monoacylglycerol lipase from thermophilic Geobacillus sp. 12AMOR | ||||||
Components | Thermostable monoacylglycerol lipase | ||||||
Keywords | HYDROLASE / lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus sp. 12AMOR1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å | ||||||
Authors | Wang, Y.H. / Lan, D.M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of monoacylglycerol lipase from thermophilic Geobacillus sp. 12AMOR Authors: Wang, Y.H. / Lan, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xks.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xks.ent.gz | 248.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xks_validation.pdf.gz | 469.8 KB | Display | wwPDB validaton report |
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Full document | 5xks_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 5xks_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 5xks_validation.cif.gz | 83 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xks ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xks | HTTPS FTP |
-Related structure data
Related structure data | 4lheS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28327.340 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus sp. 12AMOR1 (bacteria) / Gene: GARCT_00911 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: A0A0G3XXB4, acylglycerol lipase #2: 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: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 30%(w/v) Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.189→43.063 Å / Num. obs: 74128 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.843 % / Biso Wilson estimate: 34.975 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rrim(I) all: 0.152 / Χ2: 0.92 / Net I/σ(I): 11.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lhe Resolution: 2.189→43.063 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 168.42 Å2 / Biso mean: 32.6323 Å2 / Biso min: 11.75 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.189→43.063 Å
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