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- PDB-6tg7: Crystal structure of the CheY in presence of magnesium -

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Basic information

Entry
Database: PDB / ID: 6tg7
TitleCrystal structure of the CheY in presence of magnesium
ComponentsChemotaxis protein CheY
KeywordsMOTOR PROTEIN / CHEMOTAXIS / SENSORY TRANSDUCTION / PHOSPHORYLATION / FLAGELLAR ROT
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli 5-366-08_S1_C3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCamara-Artigas, A. / Salinas-Garcia, M.C. / Alba-Elena, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the CheY in presence of magnesium
Authors: Camara-Artigas, A. / Salinas-Garcia, M.C. / Alba-Elena, D.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0922
Polymers17,0681
Non-polymers241
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area6510 Å2
Unit cell
Length a, b, c (Å)45.399, 46.924, 53.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chemotaxis protein CheY /


Mass: 17067.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 5-366-08_S1_C3 (bacteria)
Gene: cheY, AB67_2120 / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A073HR60, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 6000, 0.2 MAGNESIUM ACETATE, 0.1 SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.665→34.53 Å / Num. obs: 10526 / % possible obs: 76.1 % / Redundancy: 4.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.094 / Rrim(I) all: 0.216 / Rsym value: 0.243 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.665-1.7774.81.51529211570.850.2840.6371.512.621.9
6.32-34.534.20.09111752810.9890.0470.10314.796.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBE

1jbe


Resolution: 1.65→34.53 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.2253 492 4.67 %
Rwork0.1839 --
obs0.186 10528 74.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.98 Å2 / Biso mean: 21.0734 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.65→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 1 139 1131
Biso mean--9.58 25.3 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.820.3106430.273381585825
1.82-2.080.28281150.22922481259675
2.08-2.620.23841550.19333333348898
2.62-34.530.19851790.15973407358697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.97333.8515-2.25235.9093-2.29624.00420.06770.27320.884-0.16230.10310.9393-0.56180.45050.03070.1864-0.0786-0.00740.1714-0.01570.197542.671216.62118.2978
22.35281.1508-0.85772.6171-0.62833.3913-0.1170.0123-0.1593-0.07380.1127-0.16890.07350.02580.00480.03690.01970.00590.0682-0.01210.049237.44653.37425.791
34.3745-1.18031.10041.85780.68441.2121-0.2089-0.3548-0.13940.4278-0.0147-0.28640.09751.261-0.95520.1393-0.0111-0.0330.29760.030.089337.86891.451220.6927
40.9884-0.2461-0.21751.199-0.34071.84780.0944-0.2207-0.07390.1073-0.0062-0.03740.0050.0601-0.02270.07740.00530.0060.086-0.02040.023229.36534.360516.9566
51.64742.2341-1.51333.1091-2.08161.4040.14520.1204-0.49180.1879-0.2093-0.6806-0.408-0.13550.11580.2737-0.0458-0.10080.1678-0.04980.197533.981212.293623.9711
63.328-0.068-0.13571.9651-0.10284.80020.29230.0864-0.25350.17830.0670.04190.1435-0.5735-0.09780.09810.01550.00620.10250.04840.073723.31096.89718.8557
70.7585-1.6503-0.53923.981.96612.3957-0.1955-0.0829-0.18040.47440.07250.49260.6459-1.1623-0.34570.1272-0.0231-0.030.23160.0360.086716.07319.971114.7138
80.5252-0.21570.17811.88512.34413.2552-0.112-0.0110.02140.12070.1041-0.00020.1470.3919-0.02620.09680.0115-0.0040.15240.03140.059225.26659.0536.1705
90.9071-1.1126-0.69263.50083.22637.19020.13780.22680.4432-0.37040.1897-0.3919-1.30830.0675-0.02270.1728-0.0020.04410.0982-0.00970.246330.99218.81986.112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 7 )A0 - 7
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 38 )A8 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 48 )A39 - 48
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 73 )A49 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 81 )A74 - 81
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 91 )A82 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 100 )A92 - 100
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 112 )A101 - 112
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 129 )A113 - 129

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