+Open data
-Basic information
Entry | Database: PDB / ID: 4zre | |||||||||
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Title | Crystal structure of SMG1 F278D mutant | |||||||||
Components | LIP1, secretory lipase (Family 3) | |||||||||
Keywords | HYDROLASE / mono- and diacylglycerol lipase / secretory lipase (Family 3) | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / hydrolase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Malassezia globosa (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Xu, J. / Xu, H. / Hou, S. / Liu, J. | |||||||||
Citation | Journal: Febs J. / Year: 2015 Title: Structure of product-bound SMG1 lipase: active site gating implications. Authors: Guo, S. / Xu, J. / Pavlidis, I.V. / Lan, D. / Bornscheuer, U.T. / Liu, J. / Wang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zre.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zre.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zre_validation.pdf.gz | 756.1 KB | Display | wwPDB validaton report |
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Full document | 4zre_full_validation.pdf.gz | 756.3 KB | Display | |
Data in XML | 4zre_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4zre_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/4zre ftp://data.pdbj.org/pub/pdb/validation_reports/zr/4zre | HTTPS FTP |
-Related structure data
Related structure data | 4zrdC 3uueS C: citing same article (ref.) S: Starting model for refinement |
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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: 31735.586 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-304 / Mutation: F278D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Malassezia globosa (fungus) / Strain: ATCC MYA-4612 / CBS 7966 / Gene: MGL_0797 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: A8PUY1 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CL / |
#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 Å3/Da / Density % sol: 38.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1M Bis-Tris pH5.3, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å | |||||||||||||||||||||||||||
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jun 6, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2→18.41 Å / Num. obs: 16530 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.065 / Net I/σ(I): 12.3 / Num. measured all: 84074 / Scaling rejects: 95 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UUE Resolution: 2→18.4 Å / WRfactor Rfree: 0.1986 / WRfactor Rwork: 0.1588 / FOM work R set: 0.8625 / SU R Cruickshank DPI: 0.2042 / SU Rfree: 0.164 / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 40.12 Å2 / Biso mean: 9.974 Å2 / Biso min: 3.42 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→18.4 Å
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