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- PDB-3fxu: Crystal structure of TsaR in complex with its effector p-toluenes... -

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Basic information

Entry
Database: PDB / ID: 3fxu
TitleCrystal structure of TsaR in complex with its effector p-toluenesulfonate
ComponentsLysR type regulator of tsaMBCD
KeywordsTranscription regulator / LysR-type / transcriptional regulator / LTTR / TsaR / wHTH / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / IMIDAZOLE / PARA-TOLUENE SULFONATE / HTH-type transcriptional regulator TsaR
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMonferrer, D. / Tralau, T. / Kertesz, M.A. / Kikhney, A. / Svergun, D. / Uson, I.
Citation
Journal: Mol.Microbiol. / Year: 2010
Title: Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold
Authors: Monferrer, D. / Tralau, T. / Kertesz, M.A. / Dix, I. / Sola, M. / Uson, I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: High crystallizability under air-exclusion conditions of the full-length LysR-type transcriptional regulator TsaR from Comamonas testosteroni T-2 and data-set analysis for a MIRAS structure-solution approach
Authors: Monferrer, D. / Tralau, T. / Kertesz, M.A. / Panjikar, S. / Uson, I.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR type regulator of tsaMBCD
B: LysR type regulator of tsaMBCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,77222
Polymers67,2872
Non-polymers2,48420
Water3,729207
1
A: LysR type regulator of tsaMBCD
B: LysR type regulator of tsaMBCD
hetero molecules

A: LysR type regulator of tsaMBCD
B: LysR type regulator of tsaMBCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,54344
Polymers134,5754
Non-polymers4,96840
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20500 Å2
ΔGint-86 kcal/mol
Surface area51050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.220, 52.110, 109.280
Angle α, β, γ (deg.)90.000, 111.510, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LysR type regulator of tsaMBCD / LysR-type transcriptional regulator TsaR


Mass: 33643.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: T-2 / Gene: tsaR / Plasmid: PQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): M10 / References: UniProt: P94678

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Non-polymers , 6 types, 227 molecules

#2: Chemical
ChemComp-TSU / PARA-TOLUENE SULFONATE / P-Toluenesulfonic acid


Mass: 172.202 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF DATABASE UNIPROTKB/TREMBL P94678 (P94678_COMTE) HAS A SEQUENCING ERROR.THE ...THE SEQUENCE OF DATABASE UNIPROTKB/TREMBL P94678 (P94678_COMTE) HAS A SEQUENCING ERROR.THE ADDITIONAL LEU (RESIDUE 2) AT THE N-TERMINUS OF THE STRUCTURE IS CORRECT.

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 4.6
Details: 2M Na formate, 0.1M Na acetate pH 4.6. Soaking in 250mM p-toluenesulfonate, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.9→19.75 Å / Num. all: 56186 / Num. obs: 55862 / % possible obs: 99.4 % / Redundancy: 0.99 % / Rmerge(I) obs: 0.0607 / Rsym value: 0.0453 / Net I/σ(I): 17.95
Reflection shellResolution: 1.9→1.99 Å / Rmerge(I) obs: 0.4144 / Mean I/σ(I) obs: 2.62 / Num. unique all: 7242 / Rsym value: 0.4405 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0046refinement
PDB_EXTRACT3.006data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FXQ

3fxq


Resolution: 1.95→19.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.103 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2644 5.1 %RANDOM
Rwork0.223 ---
all0.225 52003 --
obs0.225 51860 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.3 Å2 / Biso mean: 20.663 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.17 Å2
2---0.07 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 156 207 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224631
X-RAY DIFFRACTIONr_angle_refined_deg1.2752.0056307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32922.806196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53315733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9461542
X-RAY DIFFRACTIONr_chiral_restr0.0860.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213493
X-RAY DIFFRACTIONr_mcbond_it0.5571.52827
X-RAY DIFFRACTIONr_mcangle_it1.04324547
X-RAY DIFFRACTIONr_scbond_it1.74931804
X-RAY DIFFRACTIONr_scangle_it2.9064.51760
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 196 -
Rwork0.282 3572 -
all-3768 -
obs--99.66 %
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)
11.32780.38530.05410.80220.29891.93110.04770.0307-0.09420.04830.0801-0.1303-0.06380.1462-0.12790.0193-0.0093-0.0180.122-0.02290.07965.2755.66815.127
22.19220.39640.61854.5592-2.55624.3309-0.15160.03450.0883-0.43640.38190.40380.1868-0.2603-0.23020.2186-0.0028-0.05440.04810.02240.0485-0.90644.55861.967
32.33460.1133-0.16323.0661-1.02081.47510.001-0.1008-0.0610.0072-0.04360.016-0.01090.01780.04250.02020.00370.00870.0265-0.0030.0333-3.46538.52588.411
40.72911.4916-0.67178.3342-4.52643.5864-0.12470.1757-0.2018-0.85970.3386-0.11470.7332-0.1803-0.21380.3547-0.0068-0.00880.0981-0.04240.1272.28139.28961.017
53.087-0.70212.46972.6307-1.363610.17520.3368-0.2974-0.22880.1274-0.16050.03270.90840.0733-0.17630.1168-0.0348-0.0310.11460.05230.0508-5.03146.55532.377
61.85150.2597-0.15880.90390.27231.23450.0178-0.0170.05570.07610.02750.02520.04190.0062-0.04530.01390.00030.00210.03130.01310.0611-21.91956.94116.175
71.1247-0.125-0.18220.24410.2880.65680.1131-0.05650.07260.0783-0.07290.0022-0.0288-0.0879-0.04030.109-0.01850.01230.05120.00780.1112-41.40565.09426.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION2A87 - 168
3X-RAY DIFFRACTION3A169 - 263
4X-RAY DIFFRACTION4A264 - 296
5X-RAY DIFFRACTION5B1 - 73
6X-RAY DIFFRACTION6B74 - 161
7X-RAY DIFFRACTION7B162 - 296

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