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

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Basic information

Entry
Database: PDB / ID: 6zfq
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with bis-tris
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
Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9922
Polymers44,7831
Non-polymers2091
Water8,197455
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint7 kcal/mol
Surface area14780 Å2
Unit cell
Length a, b, c (Å)42.812, 106.994, 43.884
Angle α, β, γ (deg.)90.000, 110.315, 90.000
Int Tables number4
Space group name H-MP1211

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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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM bis-tris pH 5.5, 25% w/v PEG 3350. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.23 mM GlcIFG and 2.23 mM alpha-1,2-mannobiose (10 x molar ratio). 300 nl ...Details: 100 mM bis-tris pH 5.5, 25% w/v PEG 3350. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.23 mM GlcIFG and 2.23 mM alpha-1,2-mannobiose (10 x molar ratio). 300 nl droplet (150 nl protein solution, 150 nl reservoir solution). The ligand additives are probably not required for crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.2→38.41 Å / Num. obs: 114498 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.028 / Rrim(I) all: 0.057 / Net I/σ(I): 10.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5426 / CC1/2: 0.804 / Rpim(I) all: 0.485 / Rrim(I) all: 0.854 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.10.2-g9c23cb36c-releasedata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZFN

6zfn


Resolution: 1.2→38.41 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1812 5555 4.853 %
Rwork0.1409 108900 -
all0.143 --
obs-114455 99.308 %
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: 23.781 Å2
Baniso -1Baniso -2Baniso -3
1--3.612 Å20 Å21.62 Å2
2---0.784 Å2-0 Å2
3---2.508 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 14 455 3334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123074
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172691
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6584200
X-RAY DIFFRACTIONr_angle_other_deg2.3531.5746281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03921.943175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2891518
X-RAY DIFFRACTIONr_chiral_restr0.1160.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023447
X-RAY DIFFRACTIONr_gen_planes_other0.0250.02707
X-RAY DIFFRACTIONr_nbd_refined0.2180.2609
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.22525
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21459
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.29
X-RAY DIFFRACTIONr_nbd_other0.220.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.222
X-RAY DIFFRACTIONr_mcbond_it3.2712.2411411
X-RAY DIFFRACTIONr_mcbond_other3.2332.2371410
X-RAY DIFFRACTIONr_mcangle_it3.7593.3641768
X-RAY DIFFRACTIONr_mcangle_other3.8113.3661769
X-RAY DIFFRACTIONr_scbond_it4.0482.511663
X-RAY DIFFRACTIONr_scbond_other4.0472.511664
X-RAY DIFFRACTIONr_scangle_it4.7783.6532420
X-RAY DIFFRACTIONr_scangle_other4.7773.6532421
X-RAY DIFFRACTIONr_lrange_it5.05427.3553775
X-RAY DIFFRACTIONr_lrange_other4.83226.1883633
X-RAY DIFFRACTIONr_rigid_bond_restr16.00735765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.3513420.3317727X-RAY DIFFRACTION95.0188
1.231-1.2650.3183850.317735X-RAY DIFFRACTION97.7254
1.265-1.3020.3114430.2877544X-RAY DIFFRACTION99.0451
1.302-1.3420.273940.2587432X-RAY DIFFRACTION99.6562
1.342-1.3860.2683420.2397217X-RAY DIFFRACTION99.9075
1.386-1.4340.2223570.1956966X-RAY DIFFRACTION99.9727
1.434-1.4880.213420.1776759X-RAY DIFFRACTION99.7892
1.488-1.5490.1833280.1446475X-RAY DIFFRACTION99.9412
1.549-1.6180.1813400.1386194X-RAY DIFFRACTION99.9847
1.618-1.6970.1873140.1265983X-RAY DIFFRACTION99.9365
1.697-1.7890.1713100.1045611X-RAY DIFFRACTION99.9831
1.789-1.8970.1592710.0985376X-RAY DIFFRACTION100
1.897-2.0280.152820.1024990X-RAY DIFFRACTION99.9621
2.028-2.1910.1612210.1024713X-RAY DIFFRACTION100
2.191-2.40.1592430.1034299X-RAY DIFFRACTION100
2.4-2.6830.1631980.1023912X-RAY DIFFRACTION100
2.683-3.0970.1431540.113484X-RAY DIFFRACTION99.9176
3.097-3.7930.1511290.132925X-RAY DIFFRACTION100
3.793-5.360.162990.1292296X-RAY DIFFRACTION99.9166
5.36-38.410.176610.171262X-RAY DIFFRACTION99.7738

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