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- PDB-6zdc: Structure of the catalytic domain of human endo-alpha-mannosidase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zdc | |||||||||||||||
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Title | Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with nickel | |||||||||||||||
![]() | Glycoprotein endo-alpha-1,2-mannosidase | |||||||||||||||
![]() | HYDROLASE / Golgi / mannosidase / retaining | |||||||||||||||
Function / homology | ![]() 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 | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | 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 | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zdfC ![]() 6zdkC ![]() 6zdlC ![]() 6zfaC ![]() 6zfnC ![]() 6zfqC ![]() 6zj1C ![]() 6zj5C ![]() 6zj6C ![]() 5m17S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44783.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5SRI9, glycoprotein endo-alpha-1,2-mannosidase |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MIB buffer, pH 6.0. Protein at 5.5 mg/ml in 50 mM potassium phosphate, 50 mM KCl. 150 nl protein solution and 150 nl reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→135.92 Å / Num. obs: 21876 / % possible obs: 98.1 % / Redundancy: 11.4 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.061 / Rrim(I) all: 0.21 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.872 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1648 / CC1/2: 0.345 / Rpim(I) all: 0.75 / Rrim(I) all: 2.029 / % possible all: 84.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M17 Resolution: 2.251→73.103 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.171 / Average fsc free: 0.8875 / Average fsc work: 0.9025 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.199 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: 47.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.251→73.103 Å
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Refine LS restraints |
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LS refinement shell |
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