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- PDB-9g1w: NMR solution structure of the Thermus thermophilus PilF-GSPIIA domain -

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Basic information

Entry
Database: PDB / ID: 9g1w
TitleNMR solution structure of the Thermus thermophilus PilF-GSPIIA domain
ComponentsType IV pilus assembly ATPase PilB
KeywordsMOTOR PROTEIN / PilT-class / GSPII / PilF
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
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
Type IV pilus assembly ATPase PilB
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing / distance geometry
AuthorsNeissner, K. / Woehnert, J. / Hacker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Wo 901/12-1 Germany
CitationJournal: Chembiochem / Year: 2025
Title: NMR Solution Structure of the N-Terminal GSPII Domain from the Thermus Thermophilus Traffic ATPase PilF and Reconstruction of its c-di-GMP Binding Capability.
Authors: Neissner, K. / Frohnapfel, C. / Keller, H. / Duchardt-Ferner, E. / Schneider, V. / Kamjou, Z. / Averhoff, B. / Wohnert, J.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type IV pilus assembly ATPase PilB


Theoretical massNumber of molelcules
Total (without water)16,9251
Polymers16,9251
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)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Type IV pilus assembly ATPase PilB


Mass: 16924.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: pilB, TTHA0364 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SLC9
Has protein modificationN

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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
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic23D HN(CA)CB
151isotropic23D C(CO)NH
161isotropic23D H(CCO)NH
171isotropic73D HBHA(CO)NH
181isotropic23D (H)CCH-TOCSY
191isotropic23D CBCA(CO)NH
1101isotropic23D (H)CCH-TOCSY
1115isotropic63D 1H-13C NOESY aliphatic
1125isotropic63D 1H-13C NOESY aromatic
1132isotropic33D 1H-15N NOESY
1143isotropic73D 1H-13C NOESY aliphatic
1153isotropic72D 1H-13C HSQC aliphatic
1174isotropic72D 1H-13C HSQC aliphatic
1161isotropic22D 1H-13C HSQC aliphatic
1181isotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1438 uM [U-13C; U-15N] PilF1-154, 90% H2O/10% D2O13C_15N_PilF1-15490% H2O/10% D2O
solution2500 uM [U-100% 15N] PilF1-154, 90% H2O/10% D2O15N_PilF1-15490% H2O/10% D2O
solution3550 uM [U-100% 15N] PilF1-154, 90% H2O/10% D2O15N_PilF1-154_13C_methylgroups90% H2O/10% D2Oleucine and valine methylgroups (CD1/CD2) (CG1/CG2) were selectively 13C labelled.
solution4608 uM [U-15N]-Leu/Val-13C PilF1-154, 90% H2O/10% D2O15N_PilF1-154_holo-13C90% H2O/10% D2Oleucine and valine methylgroups (CD1/CD2) (CG1/CG2) were stereospecifically 13C labelled. For expression a mixture of 10%-13C-labelled and 90%-unlabelled glucose was used to achieve stereospecific labelling.
solution5335 uM [U-13C; U-15N] PilF1-154, 90% H2O/10% D2O13C_15N_PilF1-154_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
438 uMPilF1-154[U-13C; U-15N]1
500 uMPilF1-154[U-100% 15N]2
550 uMPilF1-154[U-100% 15N]3
608 uMPilF1-154[U-15N]-Leu/Val-13C4
335 uMPilF1-154[U-13C; U-15N]5
Sample conditionsIonic strength: NaCl 200 mM / Label: conditions_1 / pH: 5.8 / Pressure: AMBIENT bar / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6002
Bruker AVANCE IIIBrukerAVANCE III9503
Bruker AVANCE NEOBrukerAVANCE NEO6006
Bruker AVANCE III HDBrukerAVANCE III HD8007

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4.2Keller and Wuthrichpeak picking
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics6
simulated annealing7
distance geometry8
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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