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- PDB-8pe0: X-ray structure of the Thermus thermophilus K167L mutant of the P... -

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Basic information

Entry
Database: PDB / ID: 8pe0
TitleX-ray structure of the Thermus thermophilus K167L mutant of the 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: 1.9 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 13, 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

Downloads & links

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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)35,32824
Polymers32,5072
Non-polymers2,82122
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-96 kcal/mol
Surface area15040 Å2
Unit cell
Length a, b, c (Å)108.434, 108.434, 88.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-438-

HOH

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Components

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


Mass: 16253.540 Da / Num. of mol.: 2 / Mutation: K167L
Source method: isolated from a genetically manipulated source
Details: c-di-GMP binding domain of the ATPase enzyme PilF / 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.: 131 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M LiSO4 0.1 M Na-Acetate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.76→64.261 Å / Num. obs: 30444 / % possible obs: 99.96 % / Redundancy: 10.4 % / Biso Wilson estimate: 44.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07163 / Rpim(I) all: 0.02302 / Rrim(I) all: 0.07526 / Net I/σ(I): 15.02
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 1.713 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 3034 / CC1/2: 0.635 / Rpim(I) all: 0.5516

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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: 1.9→41.44 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.5796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 1629 5.35 %
Rwork0.1787 28806 -
obs0.1808 30435 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 133 131 2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732369
X-RAY DIFFRACTIONf_angle_d1.26033224
X-RAY DIFFRACTIONf_chiral_restr0.0655359
X-RAY DIFFRACTIONf_plane_restr0.0058399
X-RAY DIFFRACTIONf_dihedral_angle_d38.927315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.31331380.28312399X-RAY DIFFRACTION99.92
1.96-2.020.33951350.26522377X-RAY DIFFRACTION99.96
2.02-2.090.32951380.25282438X-RAY DIFFRACTION100
2.09-2.170.25751340.22912378X-RAY DIFFRACTION99.96
2.18-2.270.23891370.20022393X-RAY DIFFRACTION99.96
2.27-2.390.22261370.19132393X-RAY DIFFRACTION100
2.39-2.540.25291320.19372421X-RAY DIFFRACTION100
2.54-2.740.26411370.21242399X-RAY DIFFRACTION100
2.74-3.020.26671360.20662388X-RAY DIFFRACTION100
3.02-3.450.24461360.19992422X-RAY DIFFRACTION100
3.45-4.350.20221360.15052398X-RAY DIFFRACTION100
4.35-41.440.16351330.14862400X-RAY DIFFRACTION99.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9504604512-0.658708554225-0.1671257865557.926721875041.003681015221.37183747336-0.002187603948290.0930336112089-0.0435321213640.01256464682330.03931314567350.08086009037970.06068790660550.0847373638378-0.02844848682910.245002924026-0.0312534187514-0.02997967209280.337450509125-0.02229729340080.246118849681-9.431-17.1322.769
26.44656787418-1.946492312311.248361830732.94026954916-0.04948855675830.914104649649-0.000525133878032-0.159395834870.03979655657430.1200123150580.0177869722138-0.03558921099670.0212696230288-0.0562090714414-0.02480537528850.374769462368-0.0708209222755-0.03967187697760.4008477749630.03945392215150.340571258218-34.975-28.98721.52
32.090639562411.41875220388-0.2119270357224.773566751-1.43539751791.340620245690.430585953266-0.547326453927-0.1918956342210.874305957774-0.749073220122-0.592524709818-0.4053086822740.0416156029790.3212248571951.16420279504-0.253496627279-0.08127087528661.19955171269-0.1275073818520.950584854171-25.049-17.31624.335
42.252671525370.2012204937770.2364340141030.4102291329360.8120448090931.55433410264-0.1795673802420.536138605428-0.108936660812-0.01596876559350.07369016196750.220514132907-0.04006020835330.0627804115740.02090707183230.697991237699-0.08329574503370.0033600344050.569940682830.1601424824620.618405812402-24.498-22.06519.767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:145 OR RESID 201:201 ) )A5 - 145
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:145 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 7:145 OR RESID 201:201 ) )B7 - 145
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 7:145 OR RESID 201:201 ) )B201
5X-RAY DIFFRACTION3( CHAIN A AND RESID 202:204 ) OR ( CHAIN B AND RESID 202:205 )A202 - 204
6X-RAY DIFFRACTION3( CHAIN A AND RESID 202:204 ) OR ( CHAIN B AND RESID 202:205 )B202 - 205
7X-RAY DIFFRACTION4( CHAIN A AND RESID 205:211 ) OR ( CHAIN B AND RESID 206:211 )A205 - 211
8X-RAY DIFFRACTION4( CHAIN A AND RESID 205:211 ) OR ( CHAIN B AND RESID 206:211 )B206 - 211

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