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- PDB-5hwv: Crystal structure of PAS1 complexed with toluene -

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Basic information

Entry
Database: PDB / ID: 5hwv
TitleCrystal structure of PAS1 complexed with toluene
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 domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...PAS fold-4 / PAS fold / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TOLUENE / Sensor histidine kinase TodS
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)29,2094
Polymers29,0242
Non-polymers1842
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-4 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.359, 47.755, 126.701
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: 14512.158 Da / Num. of mol.: 2 / Fragment: PAS1 (UNP RESIDUES 43-168) / Mutation: L71M
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-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.0 M ammonium phosphate trihydrate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 30287 / % possible obs: 97.9 % / Redundancy: 13.2 % / Net I/σ(I): 48.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.049 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23087 1542 5.1 %RANDOM
Rwork0.17911 ---
obs0.18183 28907 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20 Å2
2---0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 14 308 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.9792675
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02924.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80115361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8161512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021466
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_it2.2072.776999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1535.1831247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2423.912990
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.51119.6863338
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.56131989
X-RAY DIFFRACTIONr_sphericity_free35.419587
X-RAY DIFFRACTIONr_sphericity_bonded12.73652198
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 95 -
Rwork0.149 2113 -
obs--98.79 %
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)
10.0859-0.0772-0.08540.1043-0.01810.3475-0.0072-0.0001-0.00130.0080.00640.00410.007-0.00660.00080.0086-0.0076-0.00040.01210.00620.0074-9.0195.554-30.431
20.01750.0124-0.00470.0106-0.01350.0679-0.007-0.0068-0.0028-0.0052-0.002-0.0027-0.0051-0.00190.0090.0071-0.0006-0.0020.0148-0.00050.0058-4.027-3.904-5.796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 165
2X-RAY DIFFRACTION2B43 - 167

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