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- PDB-5jgp: Crystal structure of the nitrate/nitrite sensor NarQ fragment bou... -

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Basic information

Entry
Database: PDB / ID: 5jgp
TitleCrystal structure of the nitrate/nitrite sensor NarQ fragment bound with iodide ions
ComponentsNitrate/nitrite sensor protein NarQ
KeywordsSIGNALING PROTEIN / membrane protein / sensor / histidine kinase / iodide / TRANSFERASE
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. ...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
IODIDE ION / NITRATE ION / Nitrate/nitrite sensor protein NarQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMelnikov, I. / Polovinkin, V. / Popov, A. / Gordeliy, V.
CitationJournal: Sci Adv / Year: 2017
Title: Fast iodide-SAD phasing for high-throughput membrane protein structure determination.
Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G. ...Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G.A. / Gordeliy, V. / Popov, A.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrate/nitrite sensor protein NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,39814
Polymers26,8131
Non-polymers1,58513
Water2,432135
1
A: Nitrate/nitrite sensor protein NarQ
hetero molecules

A: Nitrate/nitrite sensor protein NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,79628
Polymers53,6262
Non-polymers3,17026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_655-x+3/2,-y+1/2,z1
Buried area10160 Å2
ΔGint-66 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.241, 73.663, 236.428
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-301-

NO3

21A-301-

NO3

31A-486-

HOH

41A-533-

HOH

51A-534-

HOH

61A-535-

HOH

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Components

#1: Protein 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 (strain K12) (bacteria)
Strain: K12 / Gene: narQ, b2469, JW2453 / Production host: Escherichia coli (E. coli) / References: UniProt: P27896, histidine kinase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 47.09 %
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: 1.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2.7→59.11 Å / Num. obs: 13279 / % possible obs: 99.8 % / Redundancy: 6.73 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.03
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.78 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.24 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→59.11 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.519 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26259 349 4.9 %RANDOM
Rwork0.19016 ---
obs0.19379 6759 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å2-0 Å2-0 Å2
2---0.59 Å2-0 Å2
3----5.16 Å2
Refinement stepCycle: 1 / Resolution: 2.7→59.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 16 135 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191852
X-RAY DIFFRACTIONr_bond_other_d0.0020.021821
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9552525
X-RAY DIFFRACTIONr_angle_other_deg0.97934148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99723.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54715311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1531514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212119
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
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_it2.6554.287911
X-RAY DIFFRACTIONr_mcbond_other2.6554.286910
X-RAY DIFFRACTIONr_mcangle_it4.1756.4261139
X-RAY DIFFRACTIONr_mcangle_other4.1746.4281140
X-RAY DIFFRACTIONr_scbond_it3.1154.682941
X-RAY DIFFRACTIONr_scbond_other3.124.69938
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.156.8821380
X-RAY DIFFRACTIONr_long_range_B_refined8.10935.2542259
X-RAY DIFFRACTIONr_long_range_B_other8.00635.1782227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 31 -
Rwork0.201 490 -
obs--100 %

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