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- PDB-6xyn: Crystal structure of a proteolytic fragment of NarQ comprising se... -

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Basic information

Entry
Database: PDB / ID: 6xyn
TitleCrystal structure of a proteolytic fragment of NarQ comprising sensor and TM domains
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
NITRATE ION / Nitrate/nitrite sensor protein NarQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, 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: Crystals / Year: 2020
Title: Crystal structure of a proteolytic fragment of the sensor histidine kinase NarQ
Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Gordeliy, V.
History
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 histidine kinase NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8752
Polymers26,8131
Non-polymers621
Water1,45981
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)53,7504
Polymers53,6262
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4620 Å2
ΔGint-38 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.283, 51.283, 182.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-301-

NO3

21A-301-

NO3

31A-439-

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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / Details: 1 M KH2PO4/Na2HPO4 pH 5.2 and 5 mM NaNO3

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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: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.3→49.38 Å / Num. obs: 10245 / % possible obs: 97.8 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.035 / Rrim(I) all: 0.073 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.554 / Num. unique obs: 1015 / CC1/2: 0.772 / Rpim(I) all: 0.299 / Rrim(I) all: 0.632 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IJI

5iji


Resolution: 2.3→49.38 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.959 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 512 5 %RANDOM
Rwork0.249 ---
obs0.2507 9733 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.81 Å2 / Biso mean: 70.04 Å2 / Biso min: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 2.3→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 4 81 1328
Biso mean--40.61 52.82 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191277
X-RAY DIFFRACTIONr_bond_other_d00.021236
X-RAY DIFFRACTIONr_angle_refined_deg0.6771.951742
X-RAY DIFFRACTIONr_angle_other_deg0.52132806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3845159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77423.8657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12315204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.389157
X-RAY DIFFRACTIONr_chiral_restr0.040.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021467
X-RAY DIFFRACTIONr_gen_planes_other00.02320
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.297 34 -
Rwork0.297 724 -
obs--99.61 %

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