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- PDB-6zdk: Structure of the catalytic domain of human endo-alpha-mannosidase... -

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Basic information

Entry
Database: PDB / ID: 6zdk
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES and hexatungstotellurate(VI) TEW
ComponentsGlycoprotein endo-alpha-1,2-mannosidase
KeywordsHYDROLASE / 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
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
6-tungstotellurate(VI) / Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSobala, 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
OrganizationGrant numberCountry
European Research Council (ERC)322942 United Kingdom
Australian Research Council (ARC)DP120101396 Australia
Australian Research Council (ARC)FT130100103 Australia
Australian Research Council (ARC)DP180101957 Australia
CitationJournal: 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
DepositionJun 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 20, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8906
Polymers44,7831
Non-polymers5,1065
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint1 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.968, 128.968, 48.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Glycoprotein endo-alpha-1,2-mannosidase / hEndo / Mandaselin


Mass: 44783.094 Da / Num. of mol.: 1
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 ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O24TeW6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53.1 % / Description: hexagonal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→64.48 Å / Num. obs: 31607 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.078 / Rrim(I) all: 0.149 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2282 / CC1/2: 0.411 / Rpim(I) all: 0.45 / Rrim(I) all: 0.869 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.8.3-g908a951f-releasedata reduction
Aimless0.6.1data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZDF

6zdf


Resolution: 2→64.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.235 1554 4.936 %
Rwork0.1956 29927 -
all0.198 --
obs-31481 99.592 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.842 Å2
Baniso -1Baniso -2Baniso -3
1--1.779 Å2-0.89 Å2-0 Å2
2---1.779 Å20 Å2
3---5.772 Å2
Refinement stepCycle: LAST / Resolution: 2→64.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 109 165 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133284
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172716
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.8024764
X-RAY DIFFRACTIONr_angle_other_deg2.3181.5736328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78922.139173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8815489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7551517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023475
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02700
X-RAY DIFFRACTIONr_nbd_refined0.1940.2642
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22604
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21520
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.222
X-RAY DIFFRACTIONr_nbd_other0.2660.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.215
X-RAY DIFFRACTIONr_mcbond_it1.8043.281451
X-RAY DIFFRACTIONr_mcbond_other1.7753.2781450
X-RAY DIFFRACTIONr_mcangle_it2.7934.9121813
X-RAY DIFFRACTIONr_mcangle_other2.7984.9161814
X-RAY DIFFRACTIONr_scbond_it3.2453.9441833
X-RAY DIFFRACTIONr_scbond_other2.2243.5321663
X-RAY DIFFRACTIONr_scangle_it4.4596.22853
X-RAY DIFFRACTIONr_scangle_other3.6175.2012434
X-RAY DIFFRACTIONr_lrange_it5.31738.2533682
X-RAY DIFFRACTIONr_lrange_other5.2937.9963642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3351220.3562216X-RAY DIFFRACTION99.2781
2.052-2.1090.3671150.342101X-RAY DIFFRACTION99.6403
2.109-2.170.324980.3042082X-RAY DIFFRACTION99.6344
2.17-2.2370.3031150.2832042X-RAY DIFFRACTION99.9537
2.237-2.310.293980.2651948X-RAY DIFFRACTION99.9023
2.31-2.3910.263860.2461930X-RAY DIFFRACTION99.7526
2.391-2.4810.257940.2241832X-RAY DIFFRACTION99.7411
2.481-2.5820.254980.2071763X-RAY DIFFRACTION99.8926
2.582-2.6970.274970.2191699X-RAY DIFFRACTION99.7778
2.697-2.8290.2931010.2111603X-RAY DIFFRACTION99.4746
2.829-2.9820.25760.1941534X-RAY DIFFRACTION99.6904
2.982-3.1620.273680.2081478X-RAY DIFFRACTION99.9354
3.162-3.380.217840.1891374X-RAY DIFFRACTION99.5222
3.38-3.6510.241640.1831277X-RAY DIFFRACTION99.7026
3.651-3.9990.22550.1581198X-RAY DIFFRACTION99.6818
3.999-4.470.17390.1251093X-RAY DIFFRACTION98.951
4.47-5.1610.147540.131916X-RAY DIFFRACTION97.5855
5.161-6.3170.208340.15833X-RAY DIFFRACTION99.8848
6.317-8.9190.177280.139645X-RAY DIFFRACTION100
8.919-64.480.151280.154363X-RAY DIFFRACTION99.2386

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