+Open data
-Basic information
Entry | Database: PDB / ID: 2z5g | ||||||
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Title | Crystal structure of T1 lipase F16L mutant | ||||||
Components | Thermostable lipase | ||||||
Keywords | HYDROLASE / lipase / cation-pi interaction | ||||||
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 zalihae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matsumura, H. / Yamamoto, T. / Inoue, T. / Kai, Y. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase Authors: Matsumura, H. / Yamamoto, T. / Leow, T.C. / Mori, T. / Salleh, A.B. / Basri, M. / Inoue, T. / Kai, Y. / Rahman, R.N.Z.R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5g.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5g.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z5g_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 2z5g_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 2z5g_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 2z5g_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5g ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5g | HTTPS FTP |
-Related structure data
Related structure data | 2dsnSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43155.051 Da / Num. of mol.: 2 / Fragment: UNP residues 30-416 / Mutation: F16L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus zalihae (bacteria) / Plasmid: pGEX/T1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q842J9, triacylglycerol lipase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.5M NaCl, 0.1M KH2PO4, 0.1M NaH2PO4, 0.1M MES buffer, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.3 Å / Num. obs: 83050 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.344 / Num. unique all: 8179 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DSN Resolution: 1.8→32.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 393813.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1305 Å2 / ksol: 0.374752 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→32.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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