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- PDB-6otd: Globin sensor domain of AfGcHK in monomeric form, with imidazole -

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Basic information

Entry
Database: PDB / ID: 6otd
TitleGlobin sensor domain of AfGcHK in monomeric form, with imidazole
ComponentsGlobin-coupled histidine kinase
KeywordsTRANSFERASE / HEME / SENSOR PROTEIN / OXYGEN SENSOR / GLOBIN SENSOR DOMAIN / GLOBIN DOMAIN / IMIDAZOLE
Function / homology
Function and homology information


peptidyl-histidine phosphorylation / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / oxygen binding / heme binding / protein homodimerization activity / ATP binding / metal ion binding
Similarity search - Function
Protoglobin, globin sensor domain / Globin-sensor domain / Protoglobin / 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. ...Protoglobin, globin sensor domain / Globin-sensor domain / Protoglobin / 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. / Globin/Protoglobin / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Globin-coupled histidine kinase
Similarity search - Component
Biological speciesAnaeromyxobacter sp. Fw109-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSkalova, T. / Dohnalek, J. / Kolenko, P. / Stranava, M. / Lengalova, A. / Martinkova, M.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LM2015043 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensorAfGcHK abolishes bacterial signal transduction.
Authors: Skalova, T. / Lengalova, A. / Dohnalek, J. / Harlos, K. / Mihalcin, P. / Kolenko, P. / Stranava, M. / Blaha, J. / Shimizu, T. / Martinkova, M.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 19, 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 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Globin-coupled histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2445
Polymers18,3711
Non-polymers8734
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.440, 69.440, 113.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Globin-coupled histidine kinase / AfGcHK / Heme-based oxygen-sensor histidine kinase


Mass: 18370.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter sp. Fw109-5 (bacteria)
Strain: Fw109-5 / Gene: gchK, Anae109_2438 / Plasmid: pET-21c(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7HD43, histidine kinase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: C4 Morpheus condition (0.09M NPS ligand stock (NaNO3, Na2HPO4, (NH4)2SO4), 0.1M buffer system pH 6.5 (imidazole, MES) and 37.5% precipitant stock MPD_P1K_P3350 (MPD, PEG 1000 and PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→41.25 Å / Num. obs: 15414 / % possible obs: 99.2 % / Observed criterion σ(I): -3.7 / Redundancy: 13.9 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.32 / Num. unique obs: 902 / CC1/2: 0.703 / Rpim(I) all: 0.506 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHF

5ohf


Resolution: 1.8→41.25 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 3.52 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.127
Details: Authors state that RFREE was used in all cycles of refinement and model building. The last reciprocal refinement cycle was run against all measured reflections. The last value of RFREE ...Details: Authors state that RFREE was used in all cycles of refinement and model building. The last reciprocal refinement cycle was run against all measured reflections. The last value of RFREE before the last refinement cycle was 0.231.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 754 5 %random selection
Rwork0.182 ---
obs0.18588 15412 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.201 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.34 Å2-0 Å2
2---0.69 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 61 68 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191381
X-RAY DIFFRACTIONr_bond_other_d0.0020.021267
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9921885
X-RAY DIFFRACTIONr_angle_other_deg1.05432892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6235162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.88621.26871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37515215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8741518
X-RAY DIFFRACTIONr_chiral_restr0.1330.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021571
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02351
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7263.119624
X-RAY DIFFRACTIONr_mcbond_other2.7213.113623
X-RAY DIFFRACTIONr_mcangle_it3.7144.642782
X-RAY DIFFRACTIONr_mcangle_other3.7124.65783
X-RAY DIFFRACTIONr_scbond_it3.7393.771757
X-RAY DIFFRACTIONr_scbond_other3.7373.775758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8365.4351100
X-RAY DIFFRACTIONr_long_range_B_refined7.57136.9081670
X-RAY DIFFRACTIONr_long_range_B_other7.56136.8291664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å
RfactorNum. reflection% reflection
Rfree0.333 68 5 %
Rwork0.278 1123 -
obs--99.82 %

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