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- PDB-8pdk: X-ray structure of the Thermus thermophilus PilF-GSPIIB domain in... -

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Basic information

Entry
Database: PDB / ID: 8pdk
TitleX-ray structure of the Thermus thermophilus PilF-GSPIIB domain in the c-di-GMP bound state
Componentsc-di-GMP binding domain of the ATPase enzyme 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
ACETATE ION / Chem-C2E / ATP-binding motif-containing protein pilF
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNeissner, K. / Woehnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Wo 901/12-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structural basis for high-affinity c-di-GMP binding to the GSPII-B domain of the traffic ATPase PilF from Thermus thermophilus.
Authors: Neissner, K. / Keller, H. / Kirchner, L. / Dusterhus, S. / Duchardt-Ferner, E. / Averhoff, B. / Wohnert, J.
History
DepositionJun 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: c-di-GMP binding domain of the ATPase enzyme PilF
B: c-di-GMP binding domain of the ATPase enzyme PilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,36024
Polymers32,5392
Non-polymers2,82122
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.138, 108.138, 87.922
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-460-

HOH

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Components

#1: Protein c-di-GMP binding domain of the ATPase enzyme PilF


Mass: 16269.562 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.8 M Lithiumsulfate 0.1 M Sodiumacetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.33 Å / Num. obs: 25934 / % possible obs: 99.96 % / Redundancy: 5.2 % / Biso Wilson estimate: 37.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03878 / Rpim(I) all: 0.01886 / Rrim(I) all: 0.04317 / Net I/σ(I): 29.09
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.6646 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2624 / CC1/2: 0.779 / Rpim(I) all: 0.3309 / Rrim(I) all: 0.7432 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.33 Å / SU ML: 0.2417 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.4766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 1480 2.9 %
Rwork0.178 49601 -
obs0.1791 25928 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.62 Å2
Refinement stepCycle: LAST / Resolution: 2→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 179 178 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782341
X-RAY DIFFRACTIONf_angle_d1.0883191
X-RAY DIFFRACTIONf_chiral_restr0.0561352
X-RAY DIFFRACTIONf_plane_restr0.0057401
X-RAY DIFFRACTIONf_dihedral_angle_d22.6203308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.31991320.28784565X-RAY DIFFRACTION98.93
2.06-2.140.31021300.25894587X-RAY DIFFRACTION99.06
2.14-2.220.2941300.22684534X-RAY DIFFRACTION99.45
2.22-2.330.24371350.20714540X-RAY DIFFRACTION99.51
2.33-2.450.24421350.19324521X-RAY DIFFRACTION98.77
2.45-2.60.27531340.21014430X-RAY DIFFRACTION97.27
2.6-2.80.26931360.20374457X-RAY DIFFRACTION97.89
2.8-3.080.23631390.20434504X-RAY DIFFRACTION98.33
3.08-3.530.19461360.1764511X-RAY DIFFRACTION99.17
3.53-4.440.18241400.14574494X-RAY DIFFRACTION98.22
4.45-41.330.16381330.14684458X-RAY DIFFRACTION96.82
Refinement TLS params.Method: refined / Origin x: -22.2051116464 Å / Origin y: 22.9772054972 Å / Origin z: 6.8706395989 Å
111213212223313233
T0.259783929189 Å20.0139855382102 Å20.032144778801 Å2-0.266842437147 Å2-0.00203694770715 Å2--0.221738557076 Å2
L1.53217503282 °2-0.491152106526 °2-0.373115241876 °2-0.565842006903 °20.159592439351 °2--0.425283148805 °2
S0.0283423191708 Å °0.0484368028422 Å °0.023586303679 Å °0.0332793581688 Å °0.015896357766 Å °0.0167461011421 Å °-0.0347772938319 Å °-0.00337754382596 Å °0.000287476389412 Å °
Refinement TLS groupSelection details: all

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