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- PDB-5idj: Bifunctional histidine kinase CckA (domains DHp-CA) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5idj
TitleBifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+
ComponentsHistidine kinase
KeywordsTRANSFERASE / bifunctional / histidine kinase / phosphatase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / Histidine kinase-like ATPase, C-terminal domain ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / Histidine kinase-like ATPase, C-terminal domain / cheY-homologous receiver domain / Heat Shock Protein 90 / 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 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / histidine kinase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.02 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-138414 Switzerland
CitationJournal: Sci Adv / Year: 2016
Title: Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.
Authors: Dubey, B.N. / Lori, C. / Ozaki, S. / Fucile, G. / Plaza-Menacho, I. / Jenal, U. / Schirmer, T.
History
DepositionFeb 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 2.0Sep 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / diffrn / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.deposit_site / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_netI_over_av_sigmaI / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag
Revision 2.1Sep 21, 2022Group: Database references / Refinement description / Category: citation_author / pdbx_refine_tls_group
Item: _citation_author.identifier_ORCID / _pdbx_refine_tls_group.end_auth_seq_id
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9903
Polymers26,5381
Non-polymers4522
Water181
1
A: Histidine kinase
hetero molecules

A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9806
Polymers53,0762
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_558x,x-y,-z+7/21
Buried area5490 Å2
ΔGint-74 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.856, 164.856, 48.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Histidine kinase


Mass: 26538.248 Da / Num. of mol.: 1 / Fragment: UNP rsidues 304-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: cckA / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9X688, histidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.55 Å3/Da / Density % sol: 65.33 % / Mosaicity: 0.32 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 550 MME, 30% PEG 2000 MME, Morpheus buffer 1 pH 6.5 and Morpheus carboxylic acids

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.01→142.598 Å / Num. obs: 7413 / % possible obs: 91.4 % / Redundancy: 11.3 % / Biso Wilson estimate: 76.14 Å2 / Rsym value: 0.103 / Net I/σ(I): 15
Reflection shellResolution: 3.01→3.17 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7413 / % possible all: 51.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.55 Å47.59 Å
Translation5.55 Å47.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IDM

5idm


Resolution: 3.02→47.59 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 392 5.3 %RANDOM
Rwork0.239 7011 --
obs0.2416 7403 92.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.43 Å2 / Biso mean: 71.4027 Å2 / Biso min: 29.91 Å2
Refinement stepCycle: final / Resolution: 3.02→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 28 1 1898
Biso mean--61.59 46.69 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191911
X-RAY DIFFRACTIONr_bond_other_d0.0020.021869
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9892593
X-RAY DIFFRACTIONr_angle_other_deg1.02534271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6775237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6223.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
X-RAY DIFFRACTIONr_mcbond_it3.0192.554954
X-RAY DIFFRACTIONr_mcbond_other3.022.555953
X-RAY DIFFRACTIONr_mcangle_it4.7193.8281189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.02-3.450.36891110.30211877198877
3.45-4.350.29751400.259824872627100
4.35-47.590.26451410.213826472788100
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)
19.93745.5464-0.25286.4122-0.41112.85390.3742-0.070.00820.3854-0.2835-0.28320.0438-0.1798-0.09080.0936-0.094-0.03220.1189-0.01410.5194127.84373.3988.101
26.1279-0.0352-0.025.0591.81223.7748-0.4327-0.2072-1.38020.38010.3069-0.53240.53820.66180.12580.3988-0.11450.14320.3007-0.04011.3516120.7142.17887.12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A304 - 376
2X-RAY DIFFRACTION2A377 - 554

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