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- PDB-2y1s: Microvirin lectin -

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Basic information

Entry
Database: PDB / ID: 2y1s
TitleMicrovirin lectin
ComponentsMannan-binding lectin
KeywordsSUGAR BINDING PROTEIN / CYANOVIRIN FAMILY / CELL-CELL ATTACHMENT / ANTI-HIV PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin
Similarity search - Component
Biological speciesMicrocystis aeruginosa (bacteria)
MethodSOLUTION NMR / TORSION ANGLE, SIMULATED ANNEALING
AuthorsBewley, C.A. / Hussan, S.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Solution structure of the monovalent lectin microvirin in complex with Man(alpha)(1-2)Man provides a basis for anti-HIV activity with low toxicity.
Authors: Shahzad-ul-Hussan, S. / Gustchina, E. / Ghirlando, R. / Clore, G.M. / Bewley, C.A.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Structure summary / Version format compliance
Revision 2.0Dec 12, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED FOR SHEET AD.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannan-binding lectin


Theoretical massNumber of molelcules
Total (without water)12,1861
Polymers12,1861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein Mannan-binding lectin / Mvn protein


Mass: 12186.159 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa (bacteria) / Gene: mvn, IPF_3128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MDE2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121HN(CA)CB
131CBCA(CO)NH
141HNCO
151CC(CO)NH
161H(CCO)NH
171HBHA(CO)NH
181NOESY
191HNHA
1101HNCG
NMR detailsText: MODEL 1 IS MINIMISED AVERAGE. THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MICROVIRIN.

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 20 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: TORSION ANGLE, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 40

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