+Open data
-Basic information
Entry | Database: PDB / ID: 6zqp | ||||||
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Title | Structure of the Pmt2-MIR domain with bound ligands | ||||||
Components | PMT2 isoform 1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / carbohydrate-binding module / MIR domain / protein-O-mannosylation / beta-trefoil | ||||||
Function / homology | Function and homology information dolichyl-phosphate-mannose-protein mannosyltransferase Pmt5p-Pmt2p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked mannosylation / protein exit from endoplasmic reticulum / protein O-linked glycosylation / ERAD pathway ...dolichyl-phosphate-mannose-protein mannosyltransferase Pmt5p-Pmt2p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked mannosylation / protein exit from endoplasmic reticulum / protein O-linked glycosylation / ERAD pathway / membrane => GO:0016020 / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Wild, K. / Chiapparino, A. / Hackmann, Y. / Mortensen, S. / Sinning, I. | ||||||
Funding support | 1items
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Citation | Journal: Elife / Year: 2020 Title: Functional implications of MIR domains in protein O -mannosylation. Authors: Chiapparino, A. / Grbavac, A. / Jonker, H.R. / Hackmann, Y. / Mortensen, S. / Zatorska, E. / Schott, A. / Stier, G. / Saxena, K. / Wild, K. / Schwalbe, H. / Strahl, S. / Sinning, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zqp.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zqp.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 6zqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zqp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6zqp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6zqp_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6zqp_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/6zqp ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zqp | HTTPS FTP |
-Related structure data
Related structure data | 6zqqC 3malS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24729.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PMT2, GI526_G0000041 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PTF1, UniProt: P31382*PLUS | ||||||
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#2: Chemical | ChemComp-PG4 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.7 M AS, 1.7% (v/v) PEG400, 0.085 M HEPES pH 7.5, 15% (v/v) glycerol |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30.472 Å / Num. obs: 61507 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.998 / Net I/σ(I): 13.45 |
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique obs: 6045 / CC1/2: 0.527 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mal Resolution: 1.6→30.472 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.3 Å2 / Biso mean: 31.5258 Å2 / Biso min: 14.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→30.472 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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