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- PDB-7lkm: The PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilu... -

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Basic information

Entry
Database: PDB / ID: 7lkm
TitleThe PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilus from Xanthomonas citri
Components
  • Pilus biogenesis protein
  • Type IV fimbriae assembly protein
KeywordsTRANSPORT PROTEIN / Type IV pilus
Function / homology
Function and homology information


pilus assembly / cyclic-di-GMP binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ATPase, type IV, pilus assembly, PilB / Type II secretion system protein GspE, N-terminal / MshEN domain / predicted glycosyltransferase like domains / Type II secretion system protein GspE, N-terminal superfamily / PilZ domain / PilZ domain / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein ...ATPase, type IV, pilus assembly, PilB / Type II secretion system protein GspE, N-terminal / MshEN domain / predicted glycosyltransferase like domains / Type II secretion system protein GspE, N-terminal superfamily / PilZ domain / PilZ domain / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Thrombin, subunit H / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Pilus biogenesis protein / Type IV fimbriae assembly protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLlontop, E.E. / Guzzo, C.R. / Farah, C.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/17303-7 Brazil
CitationJournal: Plos Pathog. / Year: 2021
Title: The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri.
Authors: Llontop, E.E. / Cenens, W. / Favaro, D.C. / Sgro, G.G. / Salinas, R.K. / Guzzo, C.R. / Farah, C.S.
History
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilus biogenesis protein
B: Pilus biogenesis protein
C: Type IV fimbriae assembly protein
D: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0249
Polymers62,5434
Non-polymers4805
Water7,981443
1
A: Pilus biogenesis protein
C: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5605
Polymers31,2722
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pilus biogenesis protein
D: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4644
Polymers31,2722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.063, 122.408, 62.730
Angle α, β, γ (deg.)90.000, 98.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 or resid 12 through 46...
d_2ens_1(chain "B" and ((resid 10 and (name N or name...
d_1ens_2(chain "C" and (resid 10 through 15 or (resid 16...
d_2ens_2(chain "D" and (resid 10 through 17 or resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISHISA2
d_12ens_1ILEGLNA5 - 39
d_13ens_1PHEHISA41 - 88
d_14ens_1VALASNA90 - 98
d_15ens_1LEUILEA101 - 117
d_16ens_1HISTHRA122 - 123
d_17ens_1LEUSERA125 - 153
d_21ens_1HISHISB1
d_22ens_1ILEGLNB4 - 38
d_23ens_1PHEHISB41 - 88
d_24ens_1VALASNB91 - 99
d_25ens_1LEUILEB101 - 117
d_26ens_1HISTHRB120 - 121
d_27ens_1LEUSERB124 - 152
d_11ens_2ILEASPC3 - 10
d_12ens_2PROMETC13 - 111
d_21ens_2ILEASPD2 - 9
d_22ens_2PROMETD11 - 109

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999413651728, -0.0176144565573, 0.0293612612036), (-0.0187105784826, -0.437203362327, -0.899168023354), (0.0286751982054, -0.89919016392, 0.436617432219)-52.3140021881, 57.1164020978, 38.3743069698
2given(-0.999706384388, 0.0240472590979, -0.00297898380836), (-0.00710793277323, -0.408561079593, -0.91270330422), (-0.0231651096769, -0.912414145863, 0.408612045982)-51.3548097329, 58.0941593085, 37.0166822777

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Components

#1: Protein Pilus biogenesis protein


Mass: 18828.232 Da / Num. of mol.: 2 / Fragment: Residues 12-163 / Mutation: P70S
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal His tag
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: pilB, XAC3239 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PHL2
#2: Protein Type IV fimbriae assembly protein


Mass: 12443.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: pilZ, XAC1133 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PND9
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 44979 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.1
Reflection shellResolution: 2→3.1 Å / Rmerge(I) obs: 1.25 / Num. unique obs: 4457

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PilB-PilZ_SeMet_Model

Resolution: 2→28 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.8292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 1935 4.94 %
Rwork0.1791 37220 -
obs0.1815 39155 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.23 Å2
Refinement stepCycle: LAST / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 25 443 4331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044052
X-RAY DIFFRACTIONf_angle_d1.50035524
X-RAY DIFFRACTIONf_chiral_restr0.071642
X-RAY DIFFRACTIONf_plane_restr0.0113718
X-RAY DIFFRACTIONf_dihedral_angle_d21.6593560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.30658820501
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.788191403179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32731410.262692X-RAY DIFFRACTION99.58
2.05-2.110.30291370.23722608X-RAY DIFFRACTION99.75
2.11-2.170.30041370.22362675X-RAY DIFFRACTION99.68
2.17-2.240.26651130.21122649X-RAY DIFFRACTION99.28
2.24-2.320.24961340.20072672X-RAY DIFFRACTION99.57
2.32-2.410.26361060.19042653X-RAY DIFFRACTION99.57
2.41-2.520.24711470.19062645X-RAY DIFFRACTION99.64
2.52-2.650.25011240.19012654X-RAY DIFFRACTION99.46
2.65-2.820.23491350.19312672X-RAY DIFFRACTION99.61
2.82-3.040.24231490.17952643X-RAY DIFFRACTION99.86
3.04-3.340.21931530.17622652X-RAY DIFFRACTION99.86
3.34-3.820.21841640.15162652X-RAY DIFFRACTION99.93
3.82-4.810.17431420.13972668X-RAY DIFFRACTION99.96
4.81-28.030.18811530.16752685X-RAY DIFFRACTION99.58

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