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Yorodumi- PDB-6zfn: Structure of an inactive E404Q variant of the catalytic domain of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zfn | |||||||||||||||
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Title | Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose | |||||||||||||||
Components | Glycoprotein endo-alpha-1,2-mannosidase | |||||||||||||||
Keywords | HYDROLASE / Golgi / mannosidase / retaining | |||||||||||||||
Function / homology | Function and homology information glycoprotein endo-alpha-1,2-mannosidase / glycoprotein endo-alpha-1,2-mannosidase activity / N-glycan trimming and elongation in the cis-Golgi / alpha-mannosidase activity / Golgi membrane / Golgi apparatus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||||||||
Authors | Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | |||||||||||||||
Funding support | United Kingdom, Australia, 4items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zfn.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zfn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/6zfn ftp://data.pdbj.org/pub/pdb/validation_reports/zf/6zfn | HTTPS FTP |
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-Related structure data
Related structure data | 6zdcC 6zdfSC 6zdkC 6zdlC 6zfaC 6zfqC 6zj1C 6zj5C 6zj6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4288341 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44782.109 Da / Num. of mol.: 1 / Mutation: E404Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MANEA / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5SRI9, glycoprotein endo-alpha-1,2-mannosidase |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-SO4 / |
#4: 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 | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % / Description: hard crystals |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl ...Details: 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→52.92 Å / Num. obs: 143298 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.029 / Rrim(I) all: 0.061 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5215 / CC1/2: 0.944 / Rpim(I) all: 0.15 / Rrim(I) all: 0.271 / % possible all: 71.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZDF Resolution: 1.1→52.92 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.024 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.999 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→52.92 Å
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Refine LS restraints |
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LS refinement shell |
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