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Yorodumi- PDB-3fgt: Two chain form of the 66.3 kDa protein from mouse lacking the lin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fgt | |||||||||
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Title | Two chain form of the 66.3 kDa protein from mouse lacking the linker peptide | |||||||||
Components | (Putative phospholipase B-like 2 ...) x 2 | |||||||||
Keywords | HYDROLASE / alpha beta / glycosylated / disulphide bonds / N-terminal nucleophile hydrolase fold / two chain form / Glycoprotein / Lipid degradation / Lysosome | |||||||||
Function / homology | Function and homology information phospholipase activity / phospholipid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lysosomal lumen / lysosome / extracellular region Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | |||||||||
Authors | Lakomek, K. / Dickmanns, A. / Ficner, R. | |||||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2009 Title: Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography Authors: Lakomek, K. / Dickmanns, A. / Kettwig, M. / Urlaub, H. / Ficner, R. / Luebke, T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse Authors: Lakomek, K. / Dickmanns, A. / Mueller, U. / Kollmann, K. / Deuschl, F. / Berndt, A. / Luebke, T. / Ficner, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fgt.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fgt.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/3fgt ftp://data.pdbj.org/pub/pdb/validation_reports/fg/3fgt | HTTPS FTP |
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-Related structure data
Related structure data | 3fgrC 3fgwC 3fbxS 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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Details | author states that the biological unit is unknown |
-Components
-Putative phospholipase B-like 2 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22774.531 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 47-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/RV / Gene: AAG44101 / Plasmid: PCDNA3.1/HYGRO(+) / Cell (production host): fibrosarcoma cell / Cell line (production host): HT1080 / Production host: Homo sapiens (human) References: UniProt: Q3TCN2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: Protein | Mass: 40476.836 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 249-594 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/RV / Gene: AAG44101 / Plasmid: PCDNA3.1/HYGRO(+) / Cell (production host): fibrosarcoma cell / Cell line (production host): HT1080 / Production host: Homo sapiens (human) References: UniProt: Q3TCN2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar |
-Non-polymers , 6 types, 311 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | ChemComp-NA / | #9: Chemical | ChemComp-7PE / | #10: 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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 12% (w/v) PEG 4000, 200MM NH4AC, 100mM NaAc/HAc pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.488 Å / Num. all: 31093 / Num. obs: 31031 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.5 / Num. measured all: 15401 / Num. unique all: 4544 / Rsym value: 0.459 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FBX Resolution: 2.4→29.488 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU B: 5.671 / SU ML: 0.135 / SU R Cruickshank DPI: 0.266 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.202 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.37 Å2 / Biso mean: 28.054 Å2 / Biso min: 10.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.488 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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