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- PDB-3bbg: MULTI-CONFORMER STRUCTURE OF RAGWEED POLLEN ALLERGEN FROM AMBROSI... -

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Basic information

Entry
Database: PDB / ID: 3bbg
TitleMULTI-CONFORMER STRUCTURE OF RAGWEED POLLEN ALLERGEN FROM AMBROSIA TRIFIDA V, NMR, 2 STRUCTURES
ComponentsPOLLEN ALLERGEN 5
KeywordsALLERGEN / PROTEIN ALLERGEN / SMALL HIGHLY DISULFIDE BONDED
Function / homologyAmb V Allergen / Amb V Allergen / Amb V Allergen superfamily / Ragweed group 5 pollen allergen / Amb V Allergen / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Pollen allergen Amb t 5
Function and homology information
Biological speciesAmbrosia trifida (giant ragweed)
MethodSOLUTION NMR / MULTI-CONFORMER PROBABILITY MAP REFINEMENT
AuthorsWarren, G.L. / Tuner, C.J. / Petsko, G.A. / Brunger, A.T.
Citation
Journal: To be Published
Title: A Highly Precise Solution 1H NMR Structure of Ragweed Allergen Amb. T. V
Authors: Warren, G.L. / Turner, C.J. / Petsko, G.A. / Brunger, A.T.
#1: Journal: Biochemistry / Year: 1992
Title: Determination of the Three-Dimensional Solution Structure of Ragweed Allergen Amb T V by Nuclear Magnetic Resonance Spectroscopy
Authors: Metzler, W.J. / Valentine, K. / Roebber, M. / Friedrichs, M.S. / Marsh, D.G. / Mueller, L.
#2: Journal: Mol.Immunol. / Year: 1985
Title: Ra5G, a Homologue of Ra5 in Giant Ragweed Pollen: Isolation, Hla-Dr-Associated Activity and Amino Acid Sequence
Authors: Goodfriend, L. / Choudhury, A.M. / Klapper, D.G. / Coulter, K.M. / Dorval, G. / Del Carpio, J. / Osterland, C.K.
#3: Journal: Biochemistry / Year: 1985
Title: 500-Mhz 1H NMR Studies of Ragweed Allergen Ra5
Authors: Vidusek, D.A. / Roberts, M.F. / Goodfriend, L.
History
DepositionApr 24, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLLEN ALLERGEN 5


Theoretical massNumber of molelcules
Total (without water)4,3261
Polymers4,3261
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)2 / 1
Representative

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Components

#1: Protein/peptide POLLEN ALLERGEN 5


Mass: 4325.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: POLLEN / Source: (natural) Ambrosia trifida (giant ragweed) / References: UniProt: P10414
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQFCOSY
131PCOSY
141PECOSY
151TOCSY
1613DNOESY-TOCSY
1713DTOCSY-NOESY

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Sample preparation

Sample conditionspH: 4 / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built home builtHome-builthome built501.91
Home-built home builtHome-builthome built591.12

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Processing

Software
NameVersionClassification
CNS0.3refinement
CNS0.3phasing
NMR software
NameVersionDeveloperClassification
CNS0.3BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
MSI FELIXFELIXstructure solution
NMRCompassstructure solution
RefinementMethod: MULTI-CONFORMER PROBABILITY MAP REFINEMENT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE MANUSCRIPT SUBMITTED TO JMB ABOVE.
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 2

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