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- PDB-2k46: Xenopus laevis malectin complexed with nigerose (Glcalpha1-3Glc) -

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Basic information

Entry
Database: PDB / ID: 2k46
TitleXenopus laevis malectin complexed with nigerose (Glcalpha1-3Glc)
ComponentsMGC80075 protein
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE RECOGNITION DOMAIN / Glc2-high-mannose-N-glycan / nigerose
Function / homology
Function and homology information


protein N-linked glycosylation / carbohydrate binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Malectin / Malectin domain / Malectin domain / Galactose-binding lectin / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-nigerose / Malectin-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSchallus, T.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Malectin: A Novel Carbohydrate-binding Protein of the Endoplasmic Reticulum and a Candidate Player in the Early Steps of Protein N-Glycosylation
Authors: Schallus, T. / Jaeckh, C. / Feher, K. / Palma, A.S. / Liu, Y. / Simpson, J.C. / Mackeen, M. / Stier, G. / Gibson, T.J. / Feizi, T. / Pieler, T. / Muhle-Goll, C.
History
DepositionMay 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_assembly / pdbx_struct_oper_list / struct_conn / 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_atom_id / _atom_site.label_comp_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: MGC80075 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5422
Polymers21,2001
Non-polymers3421
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MGC80075 protein


Mass: 21200.002 Da / Num. of mol.: 1 / Fragment: sequence database residues 27-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: MGC80075 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6INX3
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose / alpha-nigerose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-nigerose
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D C(CO)NH
1513D H(CCO)NH
1623D 1H-13C NOESY
1713D 1H-15N NOESY
1832D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] malectin, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] malectin, 100% D2O100% D2O
30.8 mM malectin, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMmalectin[U-100% 13C; U-100% 15N]1
0.8 mMmalectin[U-100% 13C; U-100% 15N]2
0.8 mMmalectin3
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX9002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesprocessing
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: alpha-nigerose was attached to malectin through 31 NOEs in the course of the calculation.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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