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- PDB-7ejw: Crystal structure of FleN in complex with FleQ AAA+ doamain -

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Basic information

Entry
Database: PDB / ID: 7ejw
TitleCrystal structure of FleN in complex with FleQ AAA+ doamain
Components(Transcriptional ...) x 2
KeywordsTRANSCRIPTION / Antiactivator / Activator / ATPase / FleQ / FleN
Function / homology
Function and homology information


positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / negative regulation of cell division / 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 ...positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / negative regulation of cell division / 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 / cytoplasmic side of plasma membrane / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Flagellum site-determining protein FlhG / Flagellar regulatory FleQ / Flagellar regulatory protein FleQ / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / 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 ...Flagellum site-determining protein FlhG / Flagellar regulatory FleQ / Flagellar regulatory protein FleQ / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / 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 / CheY-like superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transcriptional regulator FleQ / Antiactivator FleN
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsChanchal / Banerjee, P. / Raghav, S. / Jain, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR23844/BRB/10/1598/2017 India
CitationJournal: Sci Adv / Year: 2021
Title: The antiactivator FleN uses an allosteric mechanism to regulate sigma 54 -dependent expression of flagellar genes in Pseudomonas aeruginosa .
Authors: Banerjee, P. / Raghav, S. / Goswami, H.N. / Jain, D.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional antiactivator FleN
B: Transcriptional antiactivator FleN
C: Transcriptional regulator FleQ
D: Transcriptional regulator FleQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,40111
Polymers119,1664
Non-polymers1,2367
Water19,0061055
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-89 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.218, 153.926, 64.568
Angle α, β, γ (deg.)90.000, 95.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Transcriptional ... , 2 types, 4 molecules ABCD

#1: Protein Transcriptional antiactivator FleN / Site-determining protein


Mass: 30484.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: fleN / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD64
#2: Protein Transcriptional regulator FleQ


Mass: 29098.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: fleQ, PA1097 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XCV0

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Non-polymers , 4 types, 1062 molecules

#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1055 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10% PEG 8000, 0.1M imidazole, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.98→77 Å / Num. obs: 86189 / % possible obs: 99.5 % / Observed criterion σ(I): 1.9 / Redundancy: 3.1 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.062 / Rsym value: 0.111 / Net I/σ(I): 7.6
Reflection shellResolution: 1.98→2.02 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4574 / CC1/2: 0.556 / Rpim(I) all: 0.386 / Rrim(I) all: 0.686 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→64.319 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 4361 5.06 %
Rwork0.1788 81748 -
obs0.1808 86109 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118 Å2 / Biso mean: 31.1883 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 1.98→64.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8077 0 72 1055 9204
Biso mean--20.37 40.43 -
Num. residues----1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088292
X-RAY DIFFRACTIONf_angle_d1.03411234
X-RAY DIFFRACTIONf_chiral_restr0.061303
X-RAY DIFFRACTIONf_plane_restr0.0061456
X-RAY DIFFRACTIONf_dihedral_angle_d17.7713103
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.98-2.00250.31981470.283271699
2.0025-2.02610.29161240.25942745100
2.0261-2.05080.30881170.24862691100
2.0508-2.07670.26471440.2355278099
2.0767-2.10410.28081700.2234266199
2.1041-2.13290.28251460.223271599
2.1329-2.16340.26011990.2235267899
2.1634-2.19570.31761270.2147268699
2.1957-2.230.2731530.2121276399
2.23-2.26650.26061520.2119265799
2.2665-2.30560.24691670.1995271599
2.3056-2.34750.28211250.1996271799
2.3475-2.39270.22691290.2048275799
2.3927-2.44150.22461410.18662717100
2.4415-2.49460.19761250.17532756100
2.4946-2.55270.24681200.17492725100
2.5527-2.61650.23251490.1771270899
2.6165-2.68720.21571510.18142737100
2.6872-2.76630.22521370.18172692100
2.7663-2.85560.25431630.18292726100
2.8556-2.95770.22621730.17792721100
2.9577-3.07610.22371570.1832741100
3.0761-3.21610.2215960.18072791100
3.2161-3.38560.22091510.1658272499
3.3856-3.59770.18631540.1562713100
3.5977-3.87550.17951630.14792703100
3.8755-4.26540.17251470.14182767100
4.2654-4.88250.15851630.1402271399
4.8825-6.15060.19411230.1734275499
6.1506-64.3190.20221480.1709277999
Refinement TLS params.Method: refined / Origin x: 25.9829 Å / Origin y: 76.0525 Å / Origin z: 1.24 Å
111213212223313233
T0.0293 Å2-0.0067 Å20.0119 Å2-0.0389 Å20.0005 Å2--0.0333 Å2
L0.1553 °20.0431 °20.0835 °2-0.1819 °20.074 °2--0.1687 °2
S-0.0024 Å °0.0027 Å °0.0271 Å °0.0101 Å °-0.0134 Å °-0.0003 Å °-0.0047 Å °-0.0305 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allG312
2X-RAY DIFFRACTION1allA7 - 280
3X-RAY DIFFRACTION1allB8 - 272
4X-RAY DIFFRACTION1allC142 - 393
5X-RAY DIFFRACTION1allD142 - 395
6X-RAY DIFFRACTION1allE501
7X-RAY DIFFRACTION1allF502
8X-RAY DIFFRACTION1allM1 - 2
9X-RAY DIFFRACTION1allM3 - 4
10X-RAY DIFFRACTION1allS1 - 1083

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