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- PDB-5exp: AAA+ domain of FleQ from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5exp
TitleAAA+ domain of FleQ from Pseudomonas aeruginosa
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
Transcriptional regulator FleQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNavarro, M.V.A.S. / Sondermann, H. / Matsuyama, B.Y.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/13238-0 Brazil
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 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)29,7417
Polymers29,3011
Non-polymers4406
Water4,828268
1
A: Transcriptional regulator FleQ
hetero molecules

A: Transcriptional regulator FleQ
hetero molecules

A: Transcriptional regulator FleQ
hetero molecules

A: Transcriptional regulator FleQ
hetero molecules

A: Transcriptional regulator FleQ
hetero molecules

A: Transcriptional regulator FleQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,44642
Polymers175,8046
Non-polymers2,64236
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation6_555x-y,x,z+5/61
Unit cell
Length a, b, c (Å)104.907, 104.907, 42.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
SymmetryHelical symmetry: (Num. of operations: 6 / Rise per n subunits: 0.2 Å / Rotation per n subunits: 60 °)

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Components

#1: Protein Transcriptional regulator FleQ


Mass: 29300.684 Da / Num. of mol.: 1 / Fragment: UNP residues 137-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fleQ, PA1097 / Plasmid: pET28-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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate and 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4592 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4592 Å / Relative weight: 1
ReflectionResolution: 1.8→45.4 Å / Num. obs: 25124 / % possible obs: 99.5 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4007 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1281 5.1 %
Rwork0.168 --
obs0.1702 25118 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 26 268 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072061
X-RAY DIFFRACTIONf_angle_d1.0042778
X-RAY DIFFRACTIONf_dihedral_angle_d13.934794
X-RAY DIFFRACTIONf_chiral_restr0.041307
X-RAY DIFFRACTIONf_plane_restr0.005366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87020.27851500.2252575X-RAY DIFFRACTION98
1.8702-1.95530.24341380.1952631X-RAY DIFFRACTION99
1.9553-2.05840.23071350.18122635X-RAY DIFFRACTION99
2.0584-2.18740.21461290.17072640X-RAY DIFFRACTION100
2.1874-2.35630.22091410.16942639X-RAY DIFFRACTION100
2.3563-2.59340.22151640.16772623X-RAY DIFFRACTION100
2.5934-2.96860.22651360.16972667X-RAY DIFFRACTION100
2.9686-3.73980.20171550.15992664X-RAY DIFFRACTION100
3.7398-45.44050.17251330.15242763X-RAY DIFFRACTION100

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