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- PDB-6rrn: GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5... -

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Basic information

Entry
Database: PDB / ID: 6rrn
TitleGOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / Mannosidase / Glycoside Hydrolase
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Alpha-mannosidase 2, C-terminal sub-domain / : / Glycosyl hydrolases family 38 C-terminal sub-domain / Lysosomal alpha-mannosidase-like, central domain / Immunoglobulin-like - #1360 / Glycoside hydrolase family 38, central domain / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase family 38, N-terminal domain ...Alpha-mannosidase 2, C-terminal sub-domain / : / Glycosyl hydrolases family 38 C-terminal sub-domain / Lysosomal alpha-mannosidase-like, central domain / Immunoglobulin-like - #1360 / Glycoside hydrolase family 38, central domain / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-KFT / SUCCINIC ACID / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsArmstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. ...Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
Funding support United Kingdom, Netherlands, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
European Research CouncilERC-2011-AdG-290836 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / ...Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / van der Marel, G.M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-mannosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,07211
Polymers118,2081
Non-polymers86410
Water11,692649
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint34 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.710, 90.386, 130.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-mannosidase 2 / / Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3- ...Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase


Mass: 118208.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-IIa, GmII, CG18802 / Production host: Thysanoplusia daubei (butterflies/moths) / Variant (production host): Hi Five
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase

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Non-polymers , 5 types, 659 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-KFT / (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide


Mass: 246.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.59→90.39 Å / Num. obs: 140967 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 1.59→1.62 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6938 / CC1/2: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bub

3bub


Resolution: 1.59→74.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 7088 5 %RANDOM
Rwork0.1799 ---
obs0.1814 133775 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.05 Å2 / Biso mean: 22.518 Å2 / Biso min: 9.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å20 Å2
2--1.08 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.59→74.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 54 649 8686
Biso mean--25.85 31.33 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138402
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177584
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.64411414
X-RAY DIFFRACTIONr_angle_other_deg2.3481.57317645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97651023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98222.026469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.554151411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3151556
X-RAY DIFFRACTIONr_chiral_restr0.090.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029413
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021827
X-RAY DIFFRACTIONr_mcbond_it1.9352.2174017
X-RAY DIFFRACTIONr_mcbond_other1.9332.2174016
X-RAY DIFFRACTIONr_mcangle_it2.6243.3135032
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 537 -
Rwork0.252 9754 -
all-10291 -
obs--99.86 %

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