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- PDB-5hww: Crystal structure of PAS1 complexed with 1,2,4-TMB -

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Basic information

Entry
Database: PDB / ID: 5hww
TitleCrystal structure of PAS1 complexed with 1,2,4-TMB
ComponentsSensor histidine kinase TodS
KeywordsTRANSFERASE / PAS / Two-component signal transduction / toluene
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / cytoplasm
Similarity search - Function
PAS fold-4 / PAS fold / PAS-associated, C-terminal / PAC domain profile. / PAS domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...PAS fold-4 / PAS fold / PAS-associated, C-terminal / PAC domain profile. / PAS domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2,4-trimethylbenzene / Sensor histidine kinase TodS
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHwang, J. / Koh, S.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System.
Authors: Koh, S. / Hwang, J. / Guchhait, K. / Lee, E.G. / Kim, S.Y. / Kim, S. / Lee, S. / Chung, J.M. / Jung, H.S. / Lee, S.J. / Ryu, C.M. / Lee, S.G. / Oh, T.K. / Kwon, O. / Kim, M.H.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Sensor histidine kinase TodS
B: Sensor histidine kinase TodS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9474
Polymers28,7072
Non-polymers2402
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-12 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.387, 51.016, 100.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor histidine kinase TodS


Mass: 14353.434 Da / Num. of mol.: 2 / Fragment: PAS1 (UNP RESIDUES 43-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain F1 / ATCC 700007) (bacteria)
Strain: F1 / ATCC 700007 / Gene: todS, Pput_2872 / Production host: Escherichia coli (E. coli) / References: UniProt: A5W4E3, histidine kinase
#2: Chemical ChemComp-XBZ / 1,2,4-trimethylbenzene / 1,2,4-Trimethylbenzene


Mass: 120.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3.0 M ammonium phosphate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 173.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 17149 / % possible obs: 98.8 % / Redundancy: 13.7 % / Net I/σ(I): 49.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.857 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26941 1218 7.7 %RANDOM
Rwork0.19233 ---
obs0.19806 14675 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å20 Å2
2--0.91 Å2-0 Å2
3----1.72 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 18 154 2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.9742609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55524.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6715357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5581513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021435
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.8584.355971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3338.0631212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.945.306966
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.50326.5453159
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 93 -
Rwork0.175 1063 -
obs--97.22 %
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)
10.5435-0.147-0.02950.8439-0.17530.55490.0098-0.0718-0.03960.089-0.011-0.05480.05290.01440.00120.0218-0.0038-0.00850.01110.00990.0198-16.5645-6.287517.7733
21.13190.3098-0.47280.9507-0.16591.30230.0695-0.03190.06030.0416-0.00520.0269-0.1149-0.0047-0.06430.0125-0.00170.00310.00250.00310.0177-5.753115.23719.9945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 166
2X-RAY DIFFRACTION2B41 - 154

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