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- PDB-8pqu: NMR structure of the Thermus thermophilus PilF-GSPIIB domain in t... -

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Basic information

Entry
Database: PDB / ID: 8pqu
TitleNMR structure of the Thermus thermophilus PilF-GSPIIB domain in the apo state
ComponentsATP-binding motif-containing protein pilF
KeywordsMOTOR PROTEIN / PilT class / GSPII / ligand binding / c-di-GMP
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-binding motif-containing protein pilF
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNeissner, K. / Woehnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Wo 901/12-1 Germany
CitationJournal: To Be Published
Title: NMR structure of the Thermus thermophilus PilF-GSPIIB domain in the apo state
Authors: Neissner, K. / Woehnert, J.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding motif-containing protein pilF


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP-binding motif-containing protein pilF / c-di-GMP binding domain of the ATPase enzyme PilF


Mass: 16269.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: pilF, TT_C1622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72H73

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY aliphatic
121isotropic23D 1H-13C NOESY aromatic
132isotropic23D 1H-15N NOESY
143isotropic13D 1H-13C NOESY aliphatic
151isotropic13D HN(CA)CB
161isotropic13D HNCO
1101isotropic13D HNCA
191isotropic13D CBCA(CO)NH
181isotropic22D 1H-13C HSQC aliphatic
171isotropic22D 1H-13C HSQC aromatic
1113isotropic12D 1H-13C HSQC aliphatic
1124isotropic32D 1H-13C HSQC aliphatic
1131isotropic13D HN(CO)CA
1141isotropic23D HN(CA)CO
1151isotropic13D (H)CCH-TOCSY
1161isotropic13D C(CO)NH
1171isotropic13D H(CCO)NH
1181isotropic13D HBHA(CO)NH
1191isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1500 uM [U-13C; U-15N] PilF159-302, 90% H2O/10% D2O13C_15N_PilF159-30290% H2O/10% D2O
solution2550 uM [U-100% 15N] PilF159-302, 90% H2O/10% D2O15N_PilF159-30290% H2O/10% D2O
solution3510 uM [U-15N]-Leu/Val-13C PilF159-302, 90% H2O/10% D2O15N_PilF159-302_13C_Methylgroups90% H2O/10% D2OThe sample was uniformely 15N labeled and leucine/valine methylgroups were selectively 13C labelled
solution4490 uM [U-15N]-Leu/Val-13C-stereospecific PilF159-302, 90% H2O/10% D2O15N_PilF159-302_13C_stereospecific90% H2O/10% D2OThe sample was uniformly 15N and 13C labelled. A mixture of 10% 13C glucose and 90% unlabelled glucose was used to stereospecifically label leucine and valine methylgroups
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPilF159-302[U-13C; U-15N]1
550 uMPilF159-302[U-100% 15N]2
510 uMPilF159-302[U-15N]-Leu/Val-13C3
490 uMPilF159-302[U-15N]-Leu/Val-13C-stereospecific4
Sample conditionsIonic strength: 200 mM NaCl mM / Label: condition_1 / pH: 5.8 / Pressure: AMBIENT atm / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE NEOBrukerAVANCE NEO8002
Bruker AVANCE III HDBrukerAVANCE III HD7003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA3.98.13Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
CARAKeller and Wuthrichpeak picking
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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