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- PDB-5ohf: Globin sensor domain of AfGcHK (FeIII form) in complex with cyani... -

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Basic information

Entry
Database: PDB / ID: 5ohf
TitleGlobin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced
ComponentsGlobin-coupled histidine kinase
KeywordsTRANSFERASE / Heme / Sensor protein / Oxygen sensor / Globin sensor domain / globin domain / cyanide
Function / homology
Function and homology information


peptidyl-histidine phosphorylation / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Globin/Protoglobin / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Globin-like superfamily / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin-coupled histidine kinase
Similarity search - Component
Biological speciesAnaeromyxobacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSkalova, T. / Kolenko, P. / Dohnalek, J. / Stranava, M. / Martinkova, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation15-19883S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.1.05/1.1.00/02.109 Czech Republic
Grant Agency of the Czech Technical UniversitySGS16/246/OHK4/3T/14 Czech Republic
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction.
Authors: Stranava, M. / Man, P. / Skalova, T. / Kolenko, P. / Blaha, J. / Fojtikova, V. / Martinek, V. / Dohnalek, J. / Lengalova, A. / Rosulek, M. / Shimizu, T. / Martinkova, M.
History
DepositionJul 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Globin-coupled histidine kinase
B: Globin-coupled histidine kinase
C: Globin-coupled histidine kinase
D: Globin-coupled histidine kinase
E: Globin-coupled histidine kinase
F: Globin-coupled histidine kinase
G: Globin-coupled histidine kinase
H: Globin-coupled histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,30730
Polymers146,9678
Non-polymers5,34022
Water18,3031016
1
A: Globin-coupled histidine kinase
B: Globin-coupled histidine kinase
hetero molecules


  • defined by author&software
  • Evidence: SAXS, Rg from SAXS: 22A, Rg from structure coordinates for dimer: 20A, gel filtration, - column - Superdex 200 - buffer 20mM Tris, 150mM NaCl, pH 8,0 - molecular mass in solution (by gel ...Evidence: SAXS, Rg from SAXS: 22A, Rg from structure coordinates for dimer: 20A, gel filtration, - column - Superdex 200 - buffer 20mM Tris, 150mM NaCl, pH 8,0 - molecular mass in solution (by gel filtration) - 40000 Da (calibrated by ovalbumin - 43 kDa, bovie serum albumin - 66 kDa, aldolase - 158 kDa) - molecular mass according to aminoacid sequence - 18341 Da, equilibrium centrifugation, Analytical ultracentrifugation: buffer 20mM Tris, 150mM NaCl, pH 8,0 sw=3,090 and sw(20,w)=3.207 molecular mass in solution (by AUC) - 38999 Da molecular mass according to amino acid sequence - 18341 Da
  • 38.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,0627
Polymers36,7422
Non-polymers1,3205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-72 kcal/mol
Surface area12590 Å2
MethodPISA
2
C: Globin-coupled histidine kinase
D: Globin-coupled histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0988
Polymers36,7422
Non-polymers1,3566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-78 kcal/mol
Surface area12090 Å2
MethodPISA
3
E: Globin-coupled histidine kinase
F: Globin-coupled histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0858
Polymers36,7422
Non-polymers1,3436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-79 kcal/mol
Surface area12680 Å2
MethodPISA
4
G: Globin-coupled histidine kinase
H: Globin-coupled histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0627
Polymers36,7422
Non-polymers1,3205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-68 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.685, 77.685, 441.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 18370.861 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter sp. (strain Fw109-5) (bacteria)
Gene: gchK, Anae109_2438 / Plasmid: pET21c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7HD43, histidine kinase

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Non-polymers , 5 types, 1038 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CN
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.27 Å3/Da / Density % sol: 46 %
Description: Crystal shape - red wedge block 300x80x80 um; the crystal was soaked for 15 min in a maternal drop containing additionally 10 mM sodium dithionite.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20.7% (w/v) PEG3350, 200 mM MgCl2, 0.01 M KCN, 7.5% (v/v) glycerol, 0.1 M MMT buffer system (DL-Malic acid, MES monohydrate, Tris, NaOH, HCl), pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.17 Å / Num. obs: 127077 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 7.3 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6192 / CC1/2: 0.844 / Rpim(I) all: 0.442 / % possible all: 100

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Processing

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

5ohe


Resolution: 1.8→49.17 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.748 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23867 6224 4.9 %Random selection
Rwork0.18991 ---
obs0.19172 126873 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9821 0 366 1016 11203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911681
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210706
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.98815940
X-RAY DIFFRACTIONr_angle_other_deg0.934324425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3251353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00121.083600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.257151828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.83315155
X-RAY DIFFRACTIONr_chiral_restr0.1030.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213255
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022940
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_it1.4412.665324
X-RAY DIFFRACTIONr_mcbond_other1.4392.6595322
X-RAY DIFFRACTIONr_mcangle_it2.2393.9786641
X-RAY DIFFRACTIONr_mcangle_other2.2393.9796642
X-RAY DIFFRACTIONr_scbond_it1.892.9426357
X-RAY DIFFRACTIONr_scbond_other1.8892.9416355
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0894.3129279
X-RAY DIFFRACTIONr_long_range_B_refined4.98230.43113374
X-RAY DIFFRACTIONr_long_range_B_other4.83229.79413046
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
Rfree0.339 439 4.8 %
Rwork0.275 9223 -
obs--99.97 %

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