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- PDB-7lkq: The PilZ(delta107-117)-FimX(GGDEF-EAL) complex from Xanthomonas citri -

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Basic information

Entry
Database: PDB / ID: 7lkq
TitleThe PilZ(delta107-117)-FimX(GGDEF-EAL) complex from Xanthomonas citri
Components
  • FimX(GGDEF-EAL)
  • Type IV fimbriae assembly protein
KeywordsTRANSPORT PROTEIN / Type IV pilus
Function / homology
Function and homology information


cyclic-di-GMP binding / nucleotide binding / metal ion binding
Similarity search - Function
PilZ domain / PilZ domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...PilZ domain / PilZ domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / CheY-like superfamily / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-C2E / PAS domain S-box protein / Type IV fimbriae assembly protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 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 1.2Oct 18, 2023Group: 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: FimX(GGDEF-EAL)
B: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2189
Polymers59,0232
Non-polymers1,1957
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type IV fimbriae assembly protein
hetero molecules

A: FimX(GGDEF-EAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2189
Polymers59,0232
Non-polymers1,1957
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)96.100, 96.100, 146.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein FimX(GGDEF-EAL)


Mass: 47794.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FimX residues 255-689 (contains both GGDEF and EAL domains) preceeded by 21 residue N-terminal sequence containing 6XHis-tag. No electron density observed for GGDEF domain.
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: XAC2398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PJX9
#2: Protein Type IV fimbriae assembly protein


Mass: 11228.033 Da / Num. of mol.: 1
Mutation: lacking residues 107-117 compared to the native protein
Source method: isolated from a genetically manipulated source
Details: PilZ residues 1-106 (lacking residues 107-117)
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-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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10 mg/ml protein, 0.1 M MES pH 6.5, 1.6 M MgSO4

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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: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 9964 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 95.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 3.4→3.74 Å / Redundancy: 14 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2287 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FOU

4fou


Resolution: 3.4→49.79 Å / SU ML: 0.4971 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.0654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2813 499 5.01 %
Rwork0.2436 9462 -
obs0.2454 9961 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.44 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 72 0 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032798
X-RAY DIFFRACTIONf_angle_d1.1843814
X-RAY DIFFRACTIONf_chiral_restr0.0527419
X-RAY DIFFRACTIONf_plane_restr0.0081491
X-RAY DIFFRACTIONf_dihedral_angle_d26.8583992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.740.38651210.25422287X-RAY DIFFRACTION99.92
3.74-4.280.26711400.21652309X-RAY DIFFRACTION100
4.28-5.390.2381250.21652356X-RAY DIFFRACTION99.96
5.39-49.790.28811130.26982510X-RAY DIFFRACTION99.92

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