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

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Basic information

Entry
Database: PDB / ID: 6zdf
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES
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: 3 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
B: Glycoprotein endo-alpha-1,2-mannosidase
C: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0646
Polymers134,3493
Non-polymers7153
Water2,522140
1
A: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0212
Polymers44,7831
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0212
Polymers44,7831
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0212
Polymers44,7831
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.245, 144.245, 139.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains B C

NCS ensembles :
ID
3
1
2

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Components

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


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 ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.8.2-g5331de77-releasedata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZDC

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1429 4.748 %RANDOM
Rwork0.2153 28670 --
all0.218 ---
obs-30099 99.947 %-
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: 49.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 3→102.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8853 0 45 140 9038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0129200
X-RAY DIFFRACTIONr_angle_refined_deg1.71.64712536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96851068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26522.093516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.232151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.661551
X-RAY DIFFRACTIONr_chiral_restr0.1260.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027279
X-RAY DIFFRACTIONr_nbd_refined0.180.23957
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.27
X-RAY DIFFRACTIONr_mcbond_it2.7694.8214281
X-RAY DIFFRACTIONr_mcangle_it4.5667.2295346
X-RAY DIFFRACTIONr_scbond_it2.8994.9724919
X-RAY DIFFRACTIONr_scangle_it4.6877.3797190
X-RAY DIFFRACTIONr_lrange_it7.50263.16613836
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.0512352
X-RAY DIFFRACTIONr_ncsr_local_group_20.0850.0512271
X-RAY DIFFRACTIONr_ncsr_local_group_30.0740.0512434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0780.355920.3442083X-RAY DIFFRACTION99.9081
3.078-3.1620.366920.3392036X-RAY DIFFRACTION100
3.162-3.2540.322900.2871970X-RAY DIFFRACTION100
3.254-3.3540.3611030.2911932X-RAY DIFFRACTION100
3.354-3.4640.3461010.2821834X-RAY DIFFRACTION100
3.464-3.5850.302940.2561835X-RAY DIFFRACTION100
3.585-3.720.271850.2371718X-RAY DIFFRACTION100
3.72-3.8720.255760.2091692X-RAY DIFFRACTION100
3.872-4.0440.23780.1731623X-RAY DIFFRACTION100
4.044-4.2420.263720.1661569X-RAY DIFFRACTION100
4.242-4.4710.246970.1621451X-RAY DIFFRACTION100
4.471-4.7420.22720.1391400X-RAY DIFFRACTION100
4.742-5.0690.167660.1331320X-RAY DIFFRACTION100
5.069-5.4740.17700.1411228X-RAY DIFFRACTION100
5.474-5.9960.17590.1381157X-RAY DIFFRACTION100
5.996-6.7020.19490.1481047X-RAY DIFFRACTION100
6.702-7.7360.382290.147949X-RAY DIFFRACTION100
7.736-9.4680.202450.167801X-RAY DIFFRACTION100
9.468-13.3610.272450.241630X-RAY DIFFRACTION100
13.361-102.2050.874140.376395X-RAY DIFFRACTION100

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