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- PDB-3a0t: Catalytic domain of histidine kinase ThkA (TM1359) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3a0t
TitleCatalytic domain of histidine kinase ThkA (TM1359) in complex with ADP and Mg ion (trigonal)
ComponentsSensor protein
KeywordsTRANSFERASE / ATP-lid / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / regulation of DNA-templated transcription / ATP binding / metal ion binding
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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...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. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.91 Å
AuthorsYamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
CitationJournal: Structure / Year: 2009
Title: Structure of PAS-linked histidine kinase and the response regulator complex
Authors: Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
History
DepositionMar 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 10, 2013Group: Other
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1783
Polymers17,7261
Non-polymers4522
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.943, 72.943, 91.258
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Sensor protein / Histidine kinase ThkA


Mass: 17726.236 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1359 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X180, histidine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 5% isopropanol, 2.0M ammonium sulphate, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2006
RadiationMonochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 22342 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 51.6
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 6 / Rsym value: 0.432 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementStarting model: nucleotide free structure

Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.901 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1133 5.1 %RANDOM
Rwork0.185 ---
obs0.186 22252 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.64 Å2 / Biso mean: 26.301 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 28 108 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221363
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9941844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69724.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44315269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4721512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021011
X-RAY DIFFRACTIONr_nbd_refined0.3280.2624
X-RAY DIFFRACTIONr_nbtor_refined0.3390.2932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.216
X-RAY DIFFRACTIONr_mcbond_it3.3061.5818
X-RAY DIFFRACTIONr_mcangle_it4.25821296
X-RAY DIFFRACTIONr_scbond_it6.1643620
X-RAY DIFFRACTIONr_scangle_it9.2674.5544
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 81 -
Rwork0.211 1506 -
all-1587 -
obs--100 %

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