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- PDB-6yue: Fragment of nitrate/nitrite sensor histidine kinase NarQ (R50S va... -

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Basic information

Entry
Database: PDB / ID: 6yue
TitleFragment of nitrate/nitrite sensor histidine kinase NarQ (R50S variant)
ComponentsNitrate/nitrite sensor protein NarQ
KeywordsMEMBRANE PROTEIN / Sensor / histidine kinase
Function / homology
Function and homology information


cellular response to nitrate / cellular response to nitrite / histidine kinase / phosphorelay sensor kinase activity / nitrate assimilation / protein dimerization activity / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Nitrate/nitrite sensor protein NarQ
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGushchin, I. / Melnikov, I. / Polovinkin, V. / Yuzhakova, A. / Gordeliy, V.
Funding support Russian Federation, France, 3items
OrganizationGrant numberCountry
Russian Science Foundation18-74-10053 Russian Federation
French National Research AgencyANR-10-INSB-05-02 France
French National Research AgencyANR-10-LABX-49-01 France
CitationJournal: Int J Mol Sci / Year: 2020
Title: Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts.
Authors: Gushchin, I. / Orekhov, P. / Melnikov, I. / Polovinkin, V. / Yuzhakova, A. / Gordeliy, V.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrate/nitrite sensor protein NarQ


Theoretical massNumber of molelcules
Total (without water)26,7431
Polymers26,7431
Non-polymers00
Water1629
1
A: Nitrate/nitrite sensor protein NarQ

A: Nitrate/nitrite sensor protein NarQ


Theoretical massNumber of molelcules
Total (without water)53,4862
Polymers53,4862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area5890 Å2
ΔGint-69 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.933, 73.702, 236.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein Nitrate/nitrite sensor protein NarQ


Mass: 26742.787 Da / Num. of mol.: 1 / Mutation: R50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: narQ, b2469, JW2453 / Production host: Escherichia coli (E. coli) / References: UniProt: P27896, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / Details: 1.2 M KH2PO4/Na2HPO4 pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.4→44.7 Å / Num. obs: 6860 / % possible obs: 87.1 % / Redundancy: 4.6 % / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.595 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 490 / CC1/2: 0.843 / % possible all: 56.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iji

5iji


Resolution: 2.4→44.7 Å / Cor.coef. Fo:Fc: 0.824 / Cor.coef. Fo:Fc free: 0.694 / SU B: 13.857 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.553
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3674 337 5 %RANDOM
Rwork0.2846 ---
obs0.2885 6383 66.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.79 Å2 / Biso mean: 38.479 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 2.4→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 9 1787
Biso mean---22.22 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0191882
X-RAY DIFFRACTIONr_bond_other_d00.021851
X-RAY DIFFRACTIONr_angle_refined_deg0.581.9522584
X-RAY DIFFRACTIONr_angle_other_deg0.48734226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9525248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59123.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60215315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3121512
X-RAY DIFFRACTIONr_chiral_restr0.0330.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022186
X-RAY DIFFRACTIONr_gen_planes_other00.02470
LS refinement shellResolution: 2.401→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 3 -
Rwork0.28 69 -
all-72 -
obs--9.55 %

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