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- PDB-3a0r: Crystal structure of histidine kinase ThkA (TM1359) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3a0r
TitleCrystal structure of histidine kinase ThkA (TM1359) in complex with response regulator protein TrrA (TM1360)
Components
  • Response regulator
  • Sensor protein
KeywordsTRANSFERASE / four helix bundle / PAS fold / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Transcriptional regulatory protein WalR-like / 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 / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Transcriptional regulatory protein WalR-like / 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 / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / CheY-like superfamily / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS fold / PAS fold / Response regulator / 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 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / histidine kinase / Response regulator
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.8 Å
AuthorsYamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
Citation
Journal: 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.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: The signaling pathway in histidine kinase and the response regulator complex revealed by X-ray crystallography and solution scattering
Authors: Yamada, S. / Akiyama, S. / Sugimoto, H. / Kumita, H. / Ito, K. / Fujisawa, T. / 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: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein
B: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7213
Polymers54,5202
Non-polymers2011
Water0
1
A: Sensor protein
B: Response regulator
hetero molecules

A: Sensor protein
B: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4416
Polymers109,0404
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area8360 Å2
ΔGint-41 kcal/mol
Surface area49610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.594, 110.594, 352.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Sensor protein / / Histidine kinase ThkA


Mass: 40999.023 Da / Num. of mol.: 1 / Fragment: PAS, catalytic domain, DHp 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: Protein Response regulator / / TrrA


Mass: 13520.953 Da / Num. of mol.: 1 / Mutation: L89M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1360 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X181
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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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: 4.93 Å3/Da / Density % sol: 75.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Bis-Tris-propane pH 7.0, 1.8M sodium acetate, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97890, 1.00551, 1.00855, 0.99240
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
21.005511
31.008551
40.99241
ReflectionResolution: 3.8→50 Å / Num. obs: 11189 / % possible obs: 94.9 % / Observed criterion σ(I): -1 / Redundancy: 7.4 % / Biso Wilson estimate: 136.94 Å2 / Rsym value: 0.054 / Net I/σ(I): 22.6
Reflection shellResolution: 3.8→3.89 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.362 / % possible all: 85.1

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.8→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 280.799 / SU ML: 1.447 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.862
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN THE INITIAL MODEL BUILDING OF THIS ENTRY (3A0R), THE HIGH RESOLUTION STRUCTURES OF THE FOLLOWING FOUR STRUCTURAL PARTS WERE USED AS A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN THE INITIAL MODEL BUILDING OF THIS ENTRY (3A0R), THE HIGH RESOLUTION STRUCTURES OF THE FOLLOWING FOUR STRUCTURAL PARTS WERE USED AS A STARTING MODEL: PAS DOMAIN (3A0S), DHP DOMAIN (2C2A), CA DOMAIN (3A0T) OF THKA , AND RESPONSE REGULATOR TRRA (3A0U). THESE MODELS WERE FITTED INTO THE 3.8 A RESOLUTION MAP THAT WAS EXPERIMENTALLY OBTAINED BY MAD PHASING, AND THEN INDIVIDUAL ATOMS WERE REFINED. AMONG THESE FOUR STRUCTURAL PARTS IN THE THKA/TRRA COMPLEX, TRRA SHOWS A VERY WEAK ELECTRON DENSITY. THE LOOPS BETA1-ALPHA1, BETA2-ALPHA2, ALPHA2-BETA3, ALPHA3-BETA4 OF TRRA ARE COMPLETELY DISORDERED. THE ALPHA4 AND STRANDS BETA1, BETA2, BETA3 OF TRRA SHOW AMBIGUOUS ELECTRON DENSITY. THE DENSITY FOR THE LOOP ALPHA6-ALPHA7 OF THE DHP DOMAIN IS NOT WELL-DEFINED. THE ATOMIC MODEL OF THESE REGIONS IS NOT ACCURATELY MODELED. THE ATP-LID REGION OF THE CA DOMAIN COULD NOT BE BUILT DUE TO DISORDER, BECAUSE IT DOES NOT HAVE STABLE CONFORMATION IN THE ABSENCE OF THE NUCLEOTIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.37098 544 5 %RANDOM
Rwork0.35 ---
obs0.35094 10381 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.25 Å2 / Biso mean: 164.727 Å2 / Biso min: 121.79 Å2
Baniso -1Baniso -2Baniso -3
1-15.63 Å20 Å20 Å2
2--15.63 Å20 Å2
3----31.26 Å2
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 1 0 3709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9815059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21624.545187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44715755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6171528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022779
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.21833
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22475
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.030.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0811.52326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.14923643
X-RAY DIFFRACTIONr_scbond_it0.15231626
X-RAY DIFFRACTIONr_scangle_it0.2434.51416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 34 -
Rwork0.467 670 -
obs--94.75 %
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)
125.64396.6955-2.197310.2492-3.240318.81981.36520.5510.82111.11810.10641.3261-2.9661-0.5021-1.4716-2.63570.50660.2373-0.04150.137-1.61473.033412.0644-39.0148
215.6584.00944.839710.9616-2.91176.70480.74641.2093-0.00291.417-1.3247-1.5637-0.86240.90110.57830.76450.50020.63790.5957-0.4634-2.210624.799219.1833-3.2414
329.636-1.68660.264818.43244.180147.4399-0.6345-0.0381-1.0938-0.96281.2935-0.02674.16912.8779-0.659-3.10980.63390.0637-2.39620.0854-1.574831.68113.4361-19.8241
420.2695-1.82939.68948.270213.188829.0333-1.19841.032.33641.5502-0.91211.0871-2.38860.26442.11050.6618-0.6975-0.0407-1.25160.37290.922818.115134.5083-21.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A415 - 519
2X-RAY DIFFRACTION2A520 - 600
3X-RAY DIFFRACTION3A604 - 755
4X-RAY DIFFRACTION4B1 - 116

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