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- PDB-3bud: Golgi mannosidase II D204A catalytic nucleophile mutant with an e... -

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Basic information

Entry
Database: PDB / ID: 3bud
TitleGolgi mannosidase II D204A catalytic nucleophile mutant with an empty active site
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 38 / Glycosidase / Golgi apparatus / Membrane / Signal-anchor / Transmembrane
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
PHOSPHATE ION / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKuntz, D.A. / Rose, D.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.
Authors: Zhong, W. / Kuntz, D.A. / Ember, B. / Singh, H. / Moremen, K.W. / Rose, D.R. / Boons, G.J.
History
DepositionJan 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 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_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.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)120,3947
Polymers119,6581
Non-polymers7366
Water26,9861498
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.903, 109.478, 138.501
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 / 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-mannosidase II / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase / MAN II / Golgi alpha-mannosidase II / AMAN II


Mass: 119657.602 Da / Num. of mol.: 1 / Fragment: Catalytic domain; UNP residues 76-1108 / Mutation: D204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-II, GmII / 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 , 4 types, 1503 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1498 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsE970K CONFLICT IN UNP ENTRY Q24451

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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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR ...Details: Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 90096 / Num. obs: 89372 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.998 / Net I/σ(I): 18.8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5801 / Χ2: 1.066 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HTY

1hty


Resolution: 1.85→19.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.594 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3607 4 %RANDOM
Rwork0.157 ---
obs0.158 89235 99.04 %-
all-90096 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 44 1498 9736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218698
X-RAY DIFFRACTIONr_angle_refined_deg1.321.93811863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85923.692428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.722151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4581558
X-RAY DIFFRACTIONr_chiral_restr0.0930.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026760
X-RAY DIFFRACTIONr_nbd_refined0.2010.24467
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.21256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.253
X-RAY DIFFRACTIONr_mcbond_it0.8091.55382
X-RAY DIFFRACTIONr_mcangle_it1.22428481
X-RAY DIFFRACTIONr_scbond_it1.90533778
X-RAY DIFFRACTIONr_scangle_it2.954.53363
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 218 -
Rwork0.309 5505 -
all-5723 -
obs--87.61 %

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