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- PDB-5iji: Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in ... -

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Basic information

Entry
Database: PDB / ID: 5iji
TitleFragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in symmetric holo state
ComponentsNitrate/nitrite sensor histidine kinase NarQ
KeywordsTRANSFERASE / membrane protein / sensor / histidine kinase / nitrate
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
EICOSANE / NITRATE ION / Nitrate/nitrite sensor protein NarQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsGushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Popov, A. / Gordeliy, V.
CitationJournal: Science / Year: 2017
Title: Mechanism of transmembrane signaling by sensor histidine kinases.
Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / ...Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / Leonard, G. / Buldt, G. / Popov, A. / Gordeliy, V.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume
Revision 1.2May 8, 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

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Assembly

Deposited unit
A: Nitrate/nitrite sensor histidine kinase NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2887
Polymers26,8131
Non-polymers1,4756
Water3,099172
1
A: Nitrate/nitrite sensor histidine kinase NarQ
hetero molecules

A: Nitrate/nitrite sensor histidine kinase NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,57514
Polymers53,6262
Non-polymers2,94912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area8150 Å2
ΔGint-41 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.702, 73.830, 235.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-306-

NO3

21A-306-

NO3

31A-471-

HOH

41A-475-

HOH

51A-510-

HOH

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Components

#1: Protein Nitrate/nitrite sensor histidine kinase NarQ / Nitrate/nitrite sensor protein NarQ


Mass: 26812.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narQ, b2469, JW2453 / Production host: Escherichia coli (E. coli) / References: UniProt: P27896, histidine kinase
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.94→39.4 Å / Num. obs: 17728 / % possible obs: 98.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.5
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→39.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.718 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25416 946 5.1 %RANDOM
Rwork0.18964 ---
obs0.19277 17728 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.285 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å2-0 Å2-0 Å2
2---0.5 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: 1 / Resolution: 1.94→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 38 172 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191933
X-RAY DIFFRACTIONr_bond_other_d0.0010.021937
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.9652636
X-RAY DIFFRACTIONr_angle_other_deg0.6234420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1245248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3323.67887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77915322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3291513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022203
X-RAY DIFFRACTIONr_gen_planes_other00.02478
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4433.126929
X-RAY DIFFRACTIONr_mcbond_other3.4443.132930
X-RAY DIFFRACTIONr_mcangle_it4.3014.6611166
X-RAY DIFFRACTIONr_mcangle_other4.3074.6671167
X-RAY DIFFRACTIONr_scbond_it4.5813.6741004
X-RAY DIFFRACTIONr_scbond_other4.5833.6791002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5875.3111456
X-RAY DIFFRACTIONr_long_range_B_refined8.13326.8052452
X-RAY DIFFRACTIONr_long_range_B_other8.13626.8162453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 62 -
Rwork0.291 1280 -
obs--97.74 %

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