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- PDB-2ow7: Golgi alpha-mannosidase II complex with (1R,6S,7R,8S)-1-thioniabi... -

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Basic information

Entry
Database: PDB / ID: 2ow7
TitleGolgi alpha-mannosidase II complex with (1R,6S,7R,8S)-1-thioniabicyclo[4.3.0]nonan-7,8-diol chloride
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 38
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 / mannose metabolic process / N-glycan processing / 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 / mannose metabolic process / N-glycan processing / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / lysosome / 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-NK2 / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKuntz, D.A.
CitationJournal: Proteins / Year: 2008
Title: Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: The role of water in inhibitor binding.
Authors: Kumar, N.S. / Kuntz, D.A. / Wen, X. / Pinto, B.M. / Rose, D.R.
History
DepositionFeb 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)120,76210
Polymers119,7021
Non-polymers1,0609
Water20,0871115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.900, 108.580, 137.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 119701.617 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (Residues 76-1108)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pMTBIP_NHIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1123 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NK2 / (1R,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-7,8-DIOL


Mass: 175.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1115 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris, PEG 6K, MPD, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 22, 2007
RadiationMonochromator: Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. all: 101363 / Num. obs: 100893 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.21 % / Rmerge(I) obs: 0.0606 / Net I/σ(I): 19.8
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.14 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
SADABSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hty

1hty


Resolution: 1.77→10.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.433 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1509 1.5 %RANDOM
Rwork0.162 ---
obs0.162 100293 99.59 %-
all-101010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.853 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→10.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 59 1115 9364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0218596
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.94911701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94151045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09823.717417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.972151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3181557
X-RAY DIFFRACTIONr_chiral_restr0.1590.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026629
X-RAY DIFFRACTIONr_nbd_refined0.2150.24255
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.21018
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.251
X-RAY DIFFRACTIONr_mcbond_it1.3651.55335
X-RAY DIFFRACTIONr_mcangle_it1.99328379
X-RAY DIFFRACTIONr_scbond_it3.20433778
X-RAY DIFFRACTIONr_scangle_it4.7584.53318
LS refinement shellResolution: 1.77→1.815 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 82 -
Rwork0.23 6788 -
obs-6870 94.98 %

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