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- PDB-6rrw: GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4... -

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Basic information

Entry
Database: PDB / ID: 6rrw
TitleGOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol
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 / : / 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 / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 ...Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 / 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 families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal 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-KG5 / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)118,7613
Polymers118,2081
Non-polymers5532
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.171, 91.671, 132.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: Trichoplusia ni (cabbage looper) / Variant (production host): Hi Five
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
#2: Chemical ChemComp-KG5 / (2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol


Mass: 487.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.61 %
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: I04 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.15→75.47 Å / Num. obs: 57896 / % possible obs: 97.6 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 9.2
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4531 / CC1/2: 0.787 / % possible all: 98.8

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Processing

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

3bub


Resolution: 2.15→75.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2823 4.9 %RANDOM
Rwork0.1995 ---
obs0.2026 54910 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.39 Å2 / Biso mean: 41.175 Å2 / Biso min: 19.29 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å2-0 Å2
2--2.58 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.15→75.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8113 0 18 267 8398
Biso mean--44.1 37.98 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138355
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177526
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.64311345
X-RAY DIFFRACTIONr_angle_other_deg2.3421.57317496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.06151001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50722.146466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.361151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4891555
X-RAY DIFFRACTIONr_chiral_restr0.0730.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029313
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021800
X-RAY DIFFRACTIONr_mcbond_it3.6114.354016
X-RAY DIFFRACTIONr_mcbond_other3.6074.354015
X-RAY DIFFRACTIONr_mcangle_it5.0656.5175013
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 206 -
Rwork0.298 4093 -
all-4299 -
obs--98.35 %

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