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- PDB-1x9d: Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Compl... -

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Basic information

Entry
Database: PDB / ID: 1x9d
TitleCrystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue
ComponentsEndoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
KeywordsHYDROLASE / mannosidase / substrate analogue / glycosyl hydrolase
Function / homology
Function and homology information


mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / ERAD pathway / protein glycosylation / : ...mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / ERAD pathway / protein glycosylation / : / ER Quality Control Compartment (ERQC) / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane
Similarity search - Function
Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside / 1,4-BUTANEDIOL / Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsKaraveg, K. / Tempel, W. / Liu, Z.J. / Siriwardena, A. / Moremen, K.W. / Wang, B.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.
Authors: Karaveg, K. / Siriwardena, A. / Tempel, W. / Liu, Z.J. / Glushka, J. / Wang, B.C. / Moremen, K.W.
History
DepositionAug 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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
Remark 999SEQUENCE THERE IS STRONG EVIDENCE FOR SPONTANEOUS N-TERMINAL TRUNCATION PRIOR TO CRYSTALLIZATION. ...SEQUENCE THERE IS STRONG EVIDENCE FOR SPONTANEOUS N-TERMINAL TRUNCATION PRIOR TO CRYSTALLIZATION. HOWEVER, THE PRECISE POSITION OF THE N-TERMINUS OF THE CRYSTALLIZING PEPTIDE HAS NOT BEEN DETERMINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0285
Polymers61,4301
Non-polymers5994
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.687, 53.878, 56.234
Angle α, β, γ (deg.)89.49, 63.60, 62.61
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase / ER alpha-1 / 2-mannosidase / Mannosidase alpha class 1B member 1 / Man9GlcNAc2-specific processing ...ER alpha-1 / 2-mannosidase / Mannosidase alpha class 1B member 1 / Man9GlcNAc2-specific processing alpha-mannosidase / UNQ747/PRO1477


Mass: 61429.531 Da / Num. of mol.: 1 / Fragment: Residues 243-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAN1B1 / Production host: Pichia pastoris (fungus)
References: UniProt: Q9UKM7, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside / methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp2SH]{[(2+S)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 378 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99985 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 84600 / % possible obs: 95.5 % / Rmerge(I) obs: 0.102 / Χ2: 6.76
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
1.41-1.460.12982251.9793.2
1.46-1.520.12383732.45894.2
1.52-1.590.11383773.07294.5
1.59-1.670.1184313.8795.4
1.67-1.780.10785004.64595.7
1.78-1.910.10385046.05896.1
1.91-2.110.10285818.09496.7
2.11-2.410.10286209.85197.5
2.41-3.040.103871512.10698.2
3.04-500.098827415.07293.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0003refinement
PDB_EXTRACT1data extraction
MAR345data collection
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMI

1fmi


Resolution: 1.41→48.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.69 / SU ML: 0.029 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / ESU R Free: 0.056 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.162 8507 10.1 %RANDOM
Rwork0.144 ---
all0.146 ---
obs0.14598 76092 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.25 Å2-0.02 Å2
2---0.07 Å20.02 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.41→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 35 376 4079
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01438040.021
X-RAY DIFFRACTIONr_bond_other_d0.00234100.02
X-RAY DIFFRACTIONr_angle_refined_deg1.33751681.947
X-RAY DIFFRACTIONr_angle_other_deg0.82679313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9074515
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 2 (DEGREES)32.28317923.687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.59963315
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 4 (DEGREES)13.332015
X-RAY DIFFRACTIONr_chiral_restr0.0875720.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00541620.02
X-RAY DIFFRACTIONr_gen_planes_other0.0018010.02
X-RAY DIFFRACTIONr_nbd_refined0.227740.2
X-RAY DIFFRACTIONr_nbd_other0.16734440.2
X-RAY DIFFRACTIONNON-BONDED TORSION REFINED ATOMS (A)0.18419260.2
X-RAY DIFFRACTIONr_nbtor_other0.08220010.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0952940.2
X-RAY DIFFRACTIONPOTENTIAL METAL-ION REFINED ATOMS (A)0.04510.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.15540.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.24400.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.069200.2
X-RAY DIFFRACTIONr_mcbond_it1.71723092
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A**2)0.4999202
X-RAY DIFFRACTIONr_mcangle_it2.25736643
X-RAY DIFFRACTIONr_scbond_it2.43916892
X-RAY DIFFRACTIONr_scangle_it3.50515043
LS refinement shellResolution: 1.41→1.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 631 -
Rwork0.158 5417 -
obs--92.56 %

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