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Yorodumi- PDB-6zdf: Structure of the catalytic domain of human endo-alpha-mannosidase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zdf | |||||||||||||||
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Title | Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES | |||||||||||||||
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: 3 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 | 6zdf.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zdf.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zdf ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zdf | HTTPS FTP |
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-Related structure data
Related structure data | 6zdcSC 6zdkC 6zdlC 6zfaC 6zfnC 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 44783.094 Da / Num. of mol.: 3 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 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1 M sodium succinate pH 7.0, 1% w/v PEG-MME2000 Protein at 10 mg/ml in buffer: 25 mM HEPES pH 7.0, 200 mM NaCl 100 nl protein solution and 200 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: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→102.205 Å / Num. obs: 30161 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 41.75 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.582 / Rpim(I) all: 0.135 / Rrim(I) all: 0.611 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4300 / CC1/2: 0.253 / Rpim(I) all: 0.265 / Rrim(I) all: 1.205 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZDC Resolution: 3→102.205 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.826 / Cross valid method: THROUGHOUT / ESU R Free: 0.46
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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: 49.027 Å2
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Refinement step | Cycle: LAST / Resolution: 3→102.205 Å
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Refine LS restraints |
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LS refinement shell |
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