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- PDB-9b4v: 4F-Trp labeled Oscillatoria Agardhii Agglutinin (OAA) -

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Basic information

Entry
Database: PDB / ID: 9b4v
Title4F-Trp labeled Oscillatoria Agardhii Agglutinin (OAA)
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Beta Barrel / carbohydrate binding
Function / homologyOAA-family lectin sugar binding domain / : / OAA-family lectin sugar binding domain / carbohydrate binding / Lectin
Function and homology information
Biological speciesOscillatoria agardhii (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsRunge, B.R. / Zadorozhnyi, R.R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J. ...Runge, B.R. / Zadorozhnyi, R.R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1708773 United States
National Science Foundation (NSF, United States)CHE 0959496 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Integrating 19 F Distance Restraints for Accurate Protein Structure Determination by Magic Angle Spinning NMR Spectroscopy.
Authors: Runge, B.R. / Zadorozhnyi, R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J.A. / Gronenborn, A.M. / Polenova, T.
History
DepositionMar 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin


Theoretical massNumber of molelcules
Total (without water)14,1701
Polymers14,1701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lectin


Mass: 14169.901 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria agardhii (bacteria) / Gene: OAA, NO365_04266 / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: C0STD7
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D CORD 25 ms
121isotropic12D CORD 50 ms
131isotropic22D CORD 100 ms
141isotropic22D CORD 250 ms
151isotropic22D CORD 500 ms
161isotropic12D NCACX 50 ms
171isotropic12D NCOCX 25 ms
181isotropic13D NCACX 50 ms
191isotropic13D NCOCX 25 ms
1101isotropic22D hCH HETCOR
1111isotropic22D hNH HETCOR
1121isotropic32D 19F-19F RFDR
1131isotropic32D hCF HETCOR
1141isotropic33D hCHF HETCOR

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Sample preparation

DetailsType: single crystal
Contents: 1.2 mM NaH2PO4, 0.8 mM K2HPO4, 0.2 mM Li2SO4, 0.1 mM CAPS, 30 mg/mL [U-100% 19F]-4F-Trp, U-100% 13C, U-100% 15N] OAA, H2O
Details: Protein was buffer exchanged into 20 mM Tris-HCl, 100 mM NaCl (pH 8.0) and concentrated to 30 mg/mL for crystallization.Sample prepared by sitting drop diffusion crystallization with a 1:1 ...Details: Protein was buffer exchanged into 20 mM Tris-HCl, 100 mM NaCl (pH 8.0) and concentrated to 30 mg/mL for crystallization.Sample prepared by sitting drop diffusion crystallization with a 1:1 ratio of protein buffer to crystallization buffer.
Label: 4F-Trp,U-13C-15N-OAA / Solvent system: H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMNaH2PO4natural abundance1
0.8 mMK2HPO4natural abundance1
0.2 mMLi2SO4natural abundance1
0.1 mMCAPSnatural abundance1
30 mg/mLOAA[U-100% 19F]-4F-Trp, U-100% 13C, U-100% 15N]1
Sample conditionsDetails: 4F-Trp,U-13C-15N-OAA crystals grown in 1.2 mM NaH2PO4/0.8 mM K2HPO4 (pH 5.5), 0.2 mM Li2SO4, and 0.1 mM CAPS (pH 10.5) at pH 6.3.
Ionic strength: 2.3 mM / Label: CAPS condition / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE III HDBrukerAVANCE III HD6002
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
NMRFAM-SPARKYLee W, Tonelli M, Markley JL.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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