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- PDB-7cfv: Solution NMR structure of DnaX mini intein from Spirulina platensis -

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Basic information

Entry
Database: PDB / ID: 7cfv
TitleSolution NMR structure of DnaX mini intein from Spirulina platensis
ComponentsSpl DnaX mini-intein
KeywordsSPLICING / Spl DnaX / Intein / Protein splicing
Function / homology
Function and homology information


DNA polymerase III complex / intein-mediated protein splicing / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / ATP binding
Similarity search - Function
DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. ...DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA polymerase III subunit gamma/tau
Similarity search - Component
Biological speciesArthrospira platensis C1 (bacteria)
MethodSOLUTION NMR / Explicit water refined
AuthorsBoral, S. / Lee, W. / De, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)ECR/2016/000847 India
CitationJournal: Biochemistry / Year: 2020
Title: Structural, Dynamic, and Functional Characterization of a DnaX Mini-intein Derived from Spirulina platensis Provides Important Insights into Intein-Mediated Catalysis of Protein Splicing.
Authors: Boral, S. / Maiti, S. / Basak, A.J. / Lee, W. / De, S.
History
DepositionJun 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: 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
Revision 1.2Jun 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 1.3May 15, 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: Spl DnaX mini-intein


Theoretical massNumber of molelcules
Total (without water)15,8101
Polymers15,8101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Spl DnaX mini-intein / DNA polymerase III subunit gamma/tau


Mass: 15809.870 Da / Num. of mol.: 1 / Mutation: C2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira platensis C1 (bacteria) / Gene: dnaX, SPLC1_S033200 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: K1XG21, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
132isotropic12D 1H-13C HSQC
143isotropic12D 1H-13C HSQC
151isotropic13D 1H-15N TOCSY
162isotropic13D 1H-15N TOCSY
172isotropic13D CBCA(CO)NH
182isotropic13D HN(CA)CB
192isotropic13D HNCO
1102isotropic13D HNCA
1112isotropic13D HN(CA)CO
1122isotropic13D C(CO)NH
1132isotropic13D H(CCO)NH
1142isotropic13D HBHA(CO)NH
1152isotropic13D (H)CCH-TOCSY
1162isotropic13D 1H-15N NOESY
1172isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-100% 15N] Spl DnaX mini-intein, 93% H2O/7% D2O15N_sample93% H2O/7% D2O
solution20.7 mM [U-100% 13C; U-100% 15N] Spl DnaX mini-intein, 93% H2O/7% D2O13C_15N_sample93% H2O/7% D2O
solution30.8 mM [U-10% 13C; U-100% 15N] Spl DnaX mini-intein, 93% H2O/7% D2O10%13C_15N_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMSpl DnaX mini-intein[U-100% 15N]1
0.7 mMSpl DnaX mini-intein[U-100% 13C; U-100% 15N]2
0.8 mMSpl DnaX mini-intein[U-10% 13C; U-100% 15N]3
Sample conditionsDetails: 20 mM sodium phosphate; 50 mM sodium chloride; 0.02 % sodium azide
Ionic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYWoonghee Leechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PONDEROSAWoonghee Leestructure calculation
PONDEROSALee, W., Stark, J.L., and Markley, J.L.refinement
NMRFAM-SPARKYLee, W., Tonelli, M., and Markley, J.L.peak picking
RefinementMethod: Explicit water refined / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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