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

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Basic information

Entry
Database: PDB / ID: 6zdc
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with nickel
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
NICKEL (II) ION / Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,8422
Polymers44,7831
Non-polymers591
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.467, 86.535, 135.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.4.1-gba385ba-releasedata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1106 5.069 %RANDOM
Rwork0.1769 20711 --
all0.179 ---
obs-21817 97.764 %-
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: 47.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.734 Å2-0 Å2-0 Å2
2---2.644 Å20 Å2
3---3.378 Å2
Refinement stepCycle: LAST / Resolution: 2.251→73.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 1 183 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133007
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172628
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6554097
X-RAY DIFFRACTIONr_angle_other_deg2.3411.5756121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04121.916167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7861517
X-RAY DIFFRACTIONr_chiral_restr0.1340.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023371
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02684
X-RAY DIFFRACTIONr_nbd_refined0.2020.2634
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22557
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21492
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.220
X-RAY DIFFRACTIONr_nbd_other0.2460.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.211
X-RAY DIFFRACTIONr_mcbond_it3.4125.0021408
X-RAY DIFFRACTIONr_mcbond_other3.4084.9981407
X-RAY DIFFRACTIONr_mcangle_it5.3387.4781759
X-RAY DIFFRACTIONr_mcangle_other5.3377.4821760
X-RAY DIFFRACTIONr_scbond_it3.475.1951598
X-RAY DIFFRACTIONr_scbond_other3.4695.1981599
X-RAY DIFFRACTIONr_scangle_it5.5297.6782333
X-RAY DIFFRACTIONr_scangle_other5.5277.6812334
X-RAY DIFFRACTIONr_lrange_it8.16156.5393584
X-RAY DIFFRACTIONr_lrange_other8.11656.4553561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.251-2.310.344660.3361231X-RAY DIFFRACTION81.0625
2.31-2.3730.326830.3091353X-RAY DIFFRACTION91.1746
2.373-2.4420.312720.2881444X-RAY DIFFRACTION97.8696
2.442-2.5170.279680.2441396X-RAY DIFFRACTION99.3216
2.517-2.5990.244850.2161371X-RAY DIFFRACTION100
2.599-2.690.271600.2111343X-RAY DIFFRACTION100
2.69-2.7920.283770.2041290X-RAY DIFFRACTION99.9269
2.792-2.9060.279790.1871222X-RAY DIFFRACTION99.9232
2.906-3.0350.24590.1831181X-RAY DIFFRACTION100
3.035-3.1830.225780.1721155X-RAY DIFFRACTION100
3.183-3.3550.226430.161101X-RAY DIFFRACTION100
3.355-3.5590.236560.1891024X-RAY DIFFRACTION100
3.559-3.8040.228540.173993X-RAY DIFFRACTION100
3.804-4.1090.236410.165924X-RAY DIFFRACTION99.7932
4.109-4.50.19400.13848X-RAY DIFFRACTION100
4.5-5.0310.161320.113786X-RAY DIFFRACTION99.7561
5.031-5.8080.194450.128679X-RAY DIFFRACTION100
5.808-7.110.167270.146601X-RAY DIFFRACTION100
7.11-10.0410.153230.133480X-RAY DIFFRACTION100
10.041-73.1030.142180.213289X-RAY DIFFRACTION99.3528

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