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- PDB-8oyz: Structure of the Histidine Kinase CheA ATP-Binding domain in comp... -

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Basic information

Entry
Database: PDB / ID: 8oyz
TitleStructure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK10
ComponentsChemotaxis protein CheA
KeywordsSIGNALING PROTEIN / inhibitor / Transferase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm
Similarity search - Function
Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain ...Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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
: / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAdhav, A. / Marina, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765147European Union
CitationJournal: To Be Published
Title: Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK10
Authors: Adhav, A. / Marina, A.
History
DepositionMay 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chemotaxis protein CheA
A: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4854
Polymers42,1592
Non-polymers3262
Water2,972165
1
B: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2422
Polymers21,0791
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area17660 Å2
3
A: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2422
Polymers21,0791
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.958, 59.133, 66.837
Angle α, β, γ (deg.)90.000, 97.041, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 5 - 189 / Label seq-ID: 5 - 189

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Chemotaxis protein CheA /


Mass: 21079.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: cheA, TM_0702 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56310, histidine kinase
#2: Chemical ChemComp-WXC / 2-azanyl-7,8-dihydro-6~{H}-quinazolin-5-one


Mass: 163.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 8000 30% Ammonium acetate 0.6 M Sodium acetate 0.065 M ph 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.85→66.333 Å / Num. obs: 26744 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 23.1
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.161 / Num. unique obs: 1883 / CC1/2: 0.991 / Rpim(I) all: 0.105 / Rrim(I) all: 0.193

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→66.333 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.197 / SU B: 7.057 / SU ML: 0.107 / Average fsc free: 0.959 / Average fsc work: 0.9772 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 1282 4.796 %
Rwork0.1902 25447 -
all0.193 --
obs-26729 98.352 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.089 Å2-0 Å2-0.049 Å2
2---0.855 Å2-0 Å2
3---0.927 Å2
Refinement stepCycle: LAST / Resolution: 1.85→66.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 24 165 2872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122740
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162744
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.6453681
X-RAY DIFFRACTIONr_angle_other_deg0.711.5776340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.6534.63622
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.38202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2910535
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.45810121
X-RAY DIFFRACTIONr_chiral_restr0.1080.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.2340.2564
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22488
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21366
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.224
X-RAY DIFFRACTIONr_nbd_other0.2360.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_mcbond_it1.7841.0431372
X-RAY DIFFRACTIONr_mcbond_other1.7631.0431372
X-RAY DIFFRACTIONr_mcangle_it2.5741.8541708
X-RAY DIFFRACTIONr_mcangle_other2.5821.8561709
X-RAY DIFFRACTIONr_scbond_it3.41.5261368
X-RAY DIFFRACTIONr_scbond_other3.41.5271368
X-RAY DIFFRACTIONr_scangle_it5.1242.5821973
X-RAY DIFFRACTIONr_scangle_other5.1232.5831974
X-RAY DIFFRACTIONr_lrange_it6.55914.6243050
X-RAY DIFFRACTIONr_lrange_other6.53814.4273034
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.055054
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.131010.05007
12BX-RAY DIFFRACTIONLocal ncs0.131010.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.286940.22618830.22919850.9550.97399.5970.189
1.898-1.950.294950.21318560.21719660.9520.97599.2370.184
1.95-2.0060.253960.18517590.18818670.9640.9899.35730.161
2.006-2.0680.267880.18617410.1918470.9610.97899.02540.17
2.068-2.1360.263800.18616630.1917700.9560.97798.47460.171
2.136-2.2110.293900.20116100.20617110.9440.97499.35710.189
2.211-2.2940.226650.19116240.19216970.9660.97799.52860.178
2.294-2.3880.299710.18915210.19415980.9290.97699.62450.179
2.388-2.4940.233690.2114750.21115500.9570.9799.61290.204
2.494-2.6150.244590.18713950.18914650.9590.97899.24910.192
2.615-2.7570.262600.19513080.19814150.9590.97796.67850.205
2.757-2.9230.21680.18312440.18413220.9690.9899.24360.194
2.923-3.1250.232670.17611860.17912580.9680.9899.60250.191
3.125-3.3750.286570.19311040.19811690.950.97799.31570.211
3.375-3.6960.234500.19410210.19610770.9710.97899.44290.214
3.696-4.130.199480.176990.1729680.9780.98477.16940.195
4.13-4.7660.146380.1538200.1528600.9910.98799.76740.186
4.766-5.830.228300.1967060.1977430.9690.98499.05790.241
5.83-8.2130.298360.2375260.2415810.9520.97396.72980.275
8.213-66.3330.232210.1913060.1943280.9710.97799.69510.255
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)
10.43320.1088-0.34770.3491-0.09611.1572-0.00260.0029-0.0077-0.0075-0.01560.01080.00590.05960.01820.00290.0048-0.01320.09460.00340.0685-18.961118.372827.5211
20.99840.1831-0.24050.7509-0.19360.25150.01270.0256-0.0341-0.0361-0.00520.04270.0355-0.0066-0.00750.016-0.0051-0.0220.0885-0.00870.06141.3047-4.80097.5017
Refinement TLS groupSelection: ALL

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