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- PDB-6qrl: Crystal structure of ShkA _Rec1 in complex with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 6qrl
TitleCrystal structure of ShkA _Rec1 in complex with c-di-GMP
ComponentsHybrid kinase
KeywordsSIGNALING PROTEIN / Cyclic di-GMP / pseudo receiver domain / second messenger / hybride histidine kinase / ShkA / auto-inhibition
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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
Chem-C2E / histidine kinase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166652 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation.
Authors: Dubey, B.N. / Agustoni, E. / Bohm, R. / Kaczmarczyk, A. / Mangia, F. / von Arx, C. / Jenal, U. / Hiller, S. / Plaza-Menacho, I. / Schirmer, T.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hybrid kinase
B: Hybrid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4308
Polymers26,4762
Non-polymers2,9546
Water2,486138
1
A: Hybrid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4055
Polymers13,2381
Non-polymers2,1674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hybrid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0253
Polymers13,2381
Non-polymers7862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.110, 55.110, 179.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 243 - 358 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hybrid kinase / Sensor histidine kinase/response regulator


Mass: 13238.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: shkA, CC_0138, CC0138 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ABT2
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.5 and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 28149 / % possible obs: 94.45 % / Redundancy: 19.2 % / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.108 / Net I/σ(I): 18.18
Reflection shellResolution: 1.84→1.9 Å / Rmerge(I) obs: 5.18 / CC1/2: 0.74 / Rpim(I) all: 5.18

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QRJ

6qrj


Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.866 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 1339 5 %RANDOM
Rwork0.2073 ---
obs0.2089 25472 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.19 Å2 / Biso mean: 38.349 Å2 / Biso min: 27.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 194 138 2042
Biso mean--39.45 43.89 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131945
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171828
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6622693
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5824202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.94718.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7115264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6711523
X-RAY DIFFRACTIONr_chiral_restr0.070.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
Refine LS restraints NCS

Ens-ID: 1 / Number: 3118 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.843→1.891 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 98 -
Rwork0.338 1855 -
all-1953 -
obs--95.64 %
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)
11.7598-0.0532-0.42951.44590.63042.25490.03720.0677-0.13630.16370.0376-0.13740.10230.0271-0.07470.0814-0.0038-0.03040.0164-0.02070.11218.58629.03764.778
21.51940.5952-0.26482.51810.16273.35320.0919-0.0682-0.06380.2458-0.0045-0.1988-0.00010.1168-0.08740.0907-0.0465-0.05370.056200.058513.79552.16282.919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 401
2X-RAY DIFFRACTION2B243 - 401

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