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- PDB-5exx: AAA+ ATPase FleQ from Pseudomonas aeruginosa bound to c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 5exx
TitleAAA+ ATPase FleQ from Pseudomonas aeruginosa bound to c-di-GMP
ComponentsTranscriptional regulator FleQ
KeywordsTRANSCRIPTION / Transcription factor / AAA+ / ATPase / c-di-GMP
Function / homology
Function and homology information


positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / negative regulation of extracellular matrix assembly / positive regulation of cell-substrate adhesion / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding ...positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / negative regulation of extracellular matrix assembly / positive regulation of cell-substrate adhesion / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding
Similarity search - Function
Flagellar regulatory FleQ / Flagellar regulatory protein FleQ / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain ...Flagellar regulatory FleQ / Flagellar regulatory protein FleQ / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / Transcriptional regulator FleQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.311 Å
AuthorsNavarro, M.V.A.S. / Sondermann, H. / Krasteva, P.V.
Funding support Brazil, United States, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/13238-0 Brazil
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI097307 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa.
Authors: Matsuyama, B.Y. / Krasteva, P.V. / Baraquet, C. / Harwood, C.S. / Sondermann, H. / Navarro, M.V.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator FleQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8594
Polymers38,3821
Non-polymers1,4773
Water00
1
A: Transcriptional regulator FleQ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)239,15324
Polymers230,2926
Non-polymers8,86118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)137.836, 137.836, 172.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Transcriptional regulator FleQ


Mass: 38381.938 Da / Num. of mol.: 1 / Fragment: UNP residues 137-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fleQ, PA1097 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XCV0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 6.17 Å3/Da / Density % sol: 80.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Bis-Tris pH 6.5, 30% pentaerythritol ethoxylate (15/4 EO/OH) and 0.05 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→43.6 Å / Num. obs: 13582 / % possible obs: 88.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.9
Reflection shellResolution: 3.3→3.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1.8 / % possible all: 47.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 3.311→43.654 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 1237 4.83 %
Rwork0.2631 --
obs0.2644 13573 90.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.311→43.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 97 0 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132171
X-RAY DIFFRACTIONf_angle_d2.5362949
X-RAY DIFFRACTIONf_dihedral_angle_d21.202802
X-RAY DIFFRACTIONf_chiral_restr0.164324
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.311-3.56650.3967830.36521750X-RAY DIFFRACTION63
3.5665-3.92520.37861260.31112555X-RAY DIFFRACTION91
3.9252-4.49270.29671350.2622792X-RAY DIFFRACTION99
4.4927-5.65840.24981340.24382847X-RAY DIFFRACTION99
5.6584-43.65730.24471770.22272974X-RAY DIFFRACTION98

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