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- PDB-8pf2: Structure of the Histidine Kinase CheA ATP-Binding domain in comp... -

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Basic information

Entry
Database: PDB / ID: 8pf2
TitleStructure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK16
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
RESORCINOL / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAdhav, A. / Marina, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765147European Union
CitationJournal: Microbiol Spectr / Year: 2024
Title: Repurposing Hsp90 inhibitors as antimicrobials targeting two-component systems identifies compounds leading to loss of bacterial membrane integrity.
Authors: Fernandez-Ciruelos, B. / Albanese, M. / Adhav, A. / Solomin, V. / Ritchie-Martinez, A. / Taverne, F. / Velikova, N. / Jirgensons, A. / Marina, A. / Finn, P.W. / Wells, J.M.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,3794
Polymers42,1592
Non-polymers2202
Water50428
1
B: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1892
Polymers21,0791
Non-polymers1101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1892
Polymers21,0791
Non-polymers1101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.966, 59.120, 67.064
Angle α, β, γ (deg.)90.000, 97.277, 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: PRO / End label comp-ID: PRO / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 5 - 187 / Label seq-ID: 5 - 187

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-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 35.63 %
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: 2.1→66.524 Å / Num. obs: 18456 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.205 / Num. unique obs: 1301 / CC1/2: 0.682 / Rpim(I) all: 0.796 / Rrim(I) all: 1.451

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
REFMAC5.8.0415refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.524 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.86 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.208
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2455 946 5.129 %
Rwork0.185 17497 -
all0.188 --
obs-18443 98.605 %
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: 40.373 Å2
Baniso -1Baniso -2Baniso -3
1--1.347 Å20 Å2-1.54 Å2
2--0.805 Å2-0 Å2
3---0.906 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 16 28 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122718
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162730
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.6443650
X-RAY DIFFRACTIONr_angle_other_deg0.8311.5766305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.638520
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg19.276201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80910534
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.84810119
X-RAY DIFFRACTIONr_chiral_restr0.1120.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02551
X-RAY DIFFRACTIONr_nbd_refined0.2220.2509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22570
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21356
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3710.257
X-RAY DIFFRACTIONr_nbd_other0.2750.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3650.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2650.21
X-RAY DIFFRACTIONr_mcbond_it4.1452.7281376
X-RAY DIFFRACTIONr_mcbond_other4.142.7281376
X-RAY DIFFRACTIONr_mcangle_it5.2764.8611713
X-RAY DIFFRACTIONr_mcangle_other5.2754.8641714
X-RAY DIFFRACTIONr_scbond_it7.4493.6821342
X-RAY DIFFRACTIONr_scbond_other7.4473.6831343
X-RAY DIFFRACTIONr_scangle_it10.8676.3191937
X-RAY DIFFRACTIONr_scangle_other10.8646.3211938
X-RAY DIFFRACTIONr_lrange_it12.83340.7322915
X-RAY DIFFRACTIONr_lrange_other12.83940.7412914
X-RAY DIFFRACTIONr_ncsr_local_group_10.1640.054851
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.163590.05007
12BX-RAY DIFFRACTIONLocal ncs0.163590.05007
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
2.1-2.1550.265730.213010.20413860.960.97499.13420.184
2.155-2.2130.247750.1812120.18413030.9620.98198.77210.167
2.213-2.2780.219740.18412370.18613280.9740.9898.71990.17
2.278-2.3480.281600.17611680.1812490.960.98298.31870.161
2.348-2.4240.297560.17211650.17812380.9560.98398.62680.163
2.424-2.5090.232570.17910930.18211730.9730.98198.03920.168
2.509-2.6040.247670.1810770.18411470.9640.98199.73840.171
2.604-2.710.233600.17410440.17711110.970.98499.36990.166
2.71-2.830.203490.1639960.16510580.9750.98498.77130.161
2.83-2.9680.27550.1739550.17810250.9610.98398.53660.176
2.968-3.1290.224480.1748970.1779650.9620.98197.92750.178
3.129-3.3180.208450.1918400.1929050.970.97897.79010.204
3.318-3.5460.261410.198100.1938540.9610.97899.64870.2
3.546-3.830.252510.187490.1848040.9590.98199.50250.197
3.83-4.1940.222390.1666990.1697510.9740.98598.2690.191
4.194-4.6860.193320.1646080.1656720.9810.98495.23810.199
4.686-5.4070.275200.1935650.1955880.970.98299.48980.24
5.407-6.6110.215270.2874900.2835180.970.96399.8070.347
6.611-9.3040.19980.23680.23940.9760.97795.43150.275
9.304-66.5240.56890.1972220.2082340.8180.9798.71790.268
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)
11.01890.3791-0.39161.012-0.75052.15940.00290.0464-0.0733-0.03680.03080.00680.10290.034-0.03380.0490.00520.01970.0138-0.01660.0409-19.508718.286427.5056
22.24370.1592-0.43621.649-0.17080.74850.02920.0977-0.0992-0.0698-0.02850.05540.0759-0.0423-0.00070.0563-0.00830.01670.0076-0.00920.01851.565-5.09767.5377
Refinement TLS groupSelection: ALL

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