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Yorodumi- PDB-6qpr: Rhizomucor miehei lipase propeptide complex, Ser95/Ile96 deletion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qpr | ||||||
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Title | Rhizomucor miehei lipase propeptide complex, Ser95/Ile96 deletion mutant | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipase / propeptide / intramolecular chaperone / inhibition / deletion mutant / fungal | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Rhizomucor miehei (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Moroz, O.V. / Blagova, E. / Reiser, V. / Saikia, R. / Dalal, S. / Jorgensen, C.I. / Baunsgaard, L. / Andersen, B. / Svendsen, A. / Wilson, K.S. | ||||||
Citation | Journal: Acs Omega / Year: 2019 Title: Novel Inhibitory Function of theRhizomucor mieheiLipase Propeptide and Three-Dimensional Structures of Its Complexes with the Enzyme. Authors: Moroz, O.V. / Blagova, E. / Reiser, V. / Saikia, R. / Dalal, S. / Jorgensen, C.I. / Bhatia, V.K. / Baunsgaard, L. / Andersen, B. / Svendsen, A. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qpr.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qpr.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qpr ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qpr | HTTPS FTP |
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-Related structure data
Related structure data | 6qppSC 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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-Components
#1: Protein | Mass: 39431.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizomucor miehei (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: P19515, triacylglycerol lipase |
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#2: Sugar | ChemComp-NAG / |
#3: 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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4M Na formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30.87 Å / Num. all: 207794 / Num. obs: 55606 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.068 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / CC1/2: 0.797 / % possible all: 67.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6qpp Resolution: 1.45→30.87 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.16 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.439 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→30.87 Å
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Refine LS restraints |
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