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- PDB-6yts: Solution NMR structure of type-I ribosome-inactivating protein tr... -

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Basic information

Entry
Database: PDB / ID: 6yts
TitleSolution NMR structure of type-I ribosome-inactivating protein trichobakin (TBK)
ComponentsTrichobakin
KeywordsHYDROLASE / Ribosome-inactivating protein / N-glycosidase activity / antitumor protein / antiviral protein
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrichosanthes sp. Bac Kan 8-98 (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBritikov, V.V. / Bocharov, E.V. / Britikova, E.V. / Le, T.B.T. / Phan, C.V. / Boyko, K.M. / Arseniev, A.S. / Usanov, S.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30014 Russian Federation
CitationJournal: To Be Published
Title: Structure and dynamics of type-I ribosome-inactivating protein trichobakin (TBK)
Authors: Britikov, V.V. / Bocharov, E.V. / Britikova, E.V. / Le, T.B.T. / Phan, C.V. / Boyko, K.M. / Arseniev, A.S. / Usanov, S.A.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trichobakin


Theoretical massNumber of molelcules
Total (without water)27,2241
Polymers27,2241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10580 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Trichobakin


Mass: 27223.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes sp. Bac Kan 8-98 (plant) / Gene: TBK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LRE3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic13D CBCA(CO)NH
151isotropic23D HNCO
161isotropic23D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HBHA(CO)NH
191isotropic23D HN(CO)CA
1101isotropic23D (H)CCH-TOCSY
1111isotropic13D HNHA
1121isotropic13D HNHB
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-15N TOCSY
1151isotropic23D 1H-13C NOESY aliphatic
1161isotropic23D 1H-13C NOESY aromatic
1171isotropic13D H(CCO)NH
1181isotropic23D HN(CA)CO
1191isotropic23D HC(C)H-TOCSY aromatic
1201isotropic23D HC(C)H-COSY aromatic
1211isotropic13D CC(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-13C; U-15N] trichobakin, 90% H2O/10% D2O
Details: potassium phosphate buffer 50 mM / Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: trichobakin / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNdata analysis
CcpNmr Analysis2.4.2CCPNpeak picking
ARIA2.3Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 8
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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