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- PDB-6j7e: Crystal Structure of Central domain of FleQ in complex with ATPgS... -

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Basic information

Entry
Database: PDB / ID: 6j7e
TitleCrystal Structure of Central domain of FleQ in complex with ATPgS and Mg
ComponentsNitrogen assimilation regulatory protein
KeywordsTRANSCRIPTION / FleQ / Pseudomonas / AAA+ / NtrC
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 / positive regulation of cell-substrate adhesion / negative regulation of extracellular matrix assembly / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding ...positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / positive regulation of cell-substrate adhesion / negative regulation of extracellular matrix assembly / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / positive 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 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / 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 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transcriptional regulator FleQ / AAA domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBanerjee, P. / Chanchal / Jain, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India) India
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Sensor I Regulated ATPase Activity of FleQ Is Essential for Motility to Biofilm Transition inPseudomonas aeruginosa.
Authors: Banerjee, P. / Chanchal / Jain, D.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogen assimilation regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2404
Polymers29,6001
Non-polymers6403
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-11 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.549, 104.549, 42.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nitrogen assimilation regulatory protein / Regulatory protein / Sigma-54-dependent Fis family transcriptional regulator / Transcriptional regulator FleQ


Mass: 29599.936 Da / Num. of mol.: 1 / Fragment: Central Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ntrC_2, fleQ, ntrC_1, C8257_22345, CAZ10_06755, CGU42_27830, DZ940_07790, DZ962_01740, NCTC13719_04150, PAERUG_E15_London_28_01_14_04909, PAMH19_4438, RW109_RW109_05080
Production host: Escherichia coli (E. coli) / References: UniProt: Q51460, UniProt: G3XCV0*PLUS
#2: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 0.2M of sodium thiocyanate, 22% of PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 2.4→90.6 Å / Num. obs: 10591 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.663

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EXP

5exp


Resolution: 2.4→52.274 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 499 4.71 %
Rwork0.1875 --
obs0.1905 10587 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→52.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 38 70 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112068
X-RAY DIFFRACTIONf_angle_d1.392793
X-RAY DIFFRACTIONf_dihedral_angle_d17.011790
X-RAY DIFFRACTIONf_chiral_restr0.05310
X-RAY DIFFRACTIONf_plane_restr0.006361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4004-2.6420.33751100.25622521X-RAY DIFFRACTION100
2.642-3.02430.32431190.23372491X-RAY DIFFRACTION100
3.0243-3.81010.23891390.18992501X-RAY DIFFRACTION99
3.8101-52.28690.21951310.15642575X-RAY DIFFRACTION99

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