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- PDB-6cah: NMR-based structure of the FHA-2 domain from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 6cah
TitleNMR-based structure of the FHA-2 domain from Mycobacterium tuberculosis ABC transporter Rv1747
ComponentsABC transporter ATP-binding/permease protein Rv1747
KeywordsPROTEIN BINDING / permuted Forkhead-associated domain / beta-sandwich / phosphothreonine binding / ABC transporter
Function / homology
Function and homology information


Translocases / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / peptidoglycan-based cell wall / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. ...: / ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding/permease protein Rv1747
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHeinkel, F. / Okon, M. / Gsponer, J. / McIntosh, L.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2018
Title: Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747.
Authors: Heinkel, F. / Shen, L. / Richard-Greenblatt, M. / Okon, M. / Bui, J.M. / Gee, C.L. / Gay, L.M. / Alber, T. / Av-Gay, Y. / Gsponer, J. / McIntosh, L.P.
History
DepositionJan 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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

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Assembly

Deposited unit
A: ABC transporter ATP-binding/permease protein Rv1747


Theoretical massNumber of molelcules
Total (without water)11,6021
Polymers11,6021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein ABC transporter ATP-binding/permease protein Rv1747


Mass: 11602.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1747 / Production host: Escherichia coli (E. coli)
References: UniProt: O65934, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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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
1121isotropic12D 1H-13C HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY
1111isotropic13D H(CCO)NH
1101isotropic13D CC(CO)NH
191isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] Rv1747 FHA-2, 20 mM Sodium Phosphate, 100 mM NaCl, water
Label: 15N/13C FHA-2 NMR sample / Solvent system: water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMRv1747 FHA-2[U-100% 13C; U-100% 15N]1
20 mMSodium Phosphate1
100 mMNaCl1
Sample conditionsIonic strength: 100 mM / Label: standard FHA NMR conditions / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMReRyu, Lim, Sung and Leerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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