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- PDB-7lko: The PilB(N-terminal)-PilZ complex of the Type IV pilus from Xanth... -

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Basic information

Entry
Database: PDB / ID: 7lko
TitleThe PilB(N-terminal)-PilZ complex of the Type IV pilus from Xanthomonas citri (2.9 A)
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 / MOLECULAR REPLACEMENT / Resolution: 2.88 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,8527
Polymers62,5634
Non-polymers2883
Water28816
1
B: Pilus biogenesis protein
C: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5705
Polymers31,2822
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-39 kcal/mol
Surface area13090 Å2
MethodPISA
2
A: Pilus biogenesis protein
D: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)31,2822
Polymers31,2822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.353, 123.547, 63.539
Angle α, β, γ (deg.)90.000, 99.282, 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

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Components

#1: Protein Pilus biogenesis protein


Mass: 18838.270 Da / Num. of mol.: 2 / Fragment: Residues 12-163
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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4 mg/ml protein, 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.88→44.01 Å / Num. obs: 13503 / % possible obs: 99.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 48.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.6
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.19 / Num. unique obs: 2614 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Coot0.8.9model building
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PilB-PilZ SeMet model

Resolution: 2.88→44.01 Å / SU ML: 0.3117 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 671 4.97 %
Rwork0.1581 12832 -
obs0.1616 13503 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.72 Å2
Refinement stepCycle: LAST / Resolution: 2.88→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 15 16 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01293956
X-RAY DIFFRACTIONf_angle_d1.4545387
X-RAY DIFFRACTIONf_chiral_restr0.072630
X-RAY DIFFRACTIONf_plane_restr0.0106702
X-RAY DIFFRACTIONf_dihedral_angle_d18.7081542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.10.27471330.19922523X-RAY DIFFRACTION98.66
3.1-3.420.27461390.18692546X-RAY DIFFRACTION99.85
3.42-3.910.23071270.15632584X-RAY DIFFRACTION99.89
3.91-4.930.19751490.13332578X-RAY DIFFRACTION99.85
4.93-44.010.21451230.15462601X-RAY DIFFRACTION99.85

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