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- PDB-3fxr: Crystal structure of TsaR in complex with sulfate -

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Basic information

Entry
Database: PDB / ID: 3fxr
TitleCrystal structure of TsaR in complex with sulfate
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
ASCORBIC ACID / HTH-type transcriptional regulator TsaR
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_ref_seq_dif ...chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)68,70016
Polymers67,2872
Non-polymers1,41314
Water4,522251
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)137,40132
Polymers134,5754
Non-polymers2,82628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area18410 Å2
ΔGint-392 kcal/mol
Surface area51640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.110, 51.830, 107.990
Angle α, β, γ (deg.)90.000, 110.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 4.6
Details: 0.2M Ammonium sulfate, 25% w/v PEG 4000, 0.1M Na acetate pH 4.6, 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: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.5→19.9 Å / Num. all: 24580 / Num. obs: 24481 / % possible obs: 99.7 % / Redundancy: 1 % / Rsym value: 0.00648 / Net I/σ(I): 15.92
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 2499 / Rsym value: 0.267 / % possible all: 99.9

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Processing

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

3fxq


Resolution: 2.5→19.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.858 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.678 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS parameterization / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1251 5.1 %RANDOM
Rwork0.204 ---
all0.207 24515 --
obs0.207 24479 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.45 Å2 / Biso mean: 17.605 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.53 Å2
2--0.18 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 80 251 4903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224744
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9886462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58522.723202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85915767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6481546
X-RAY DIFFRACTIONr_chiral_restr0.0840.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213563
X-RAY DIFFRACTIONr_mcbond_it0.391.52969
X-RAY DIFFRACTIONr_mcangle_it0.76624774
X-RAY DIFFRACTIONr_scbond_it1.34431775
X-RAY DIFFRACTIONr_scangle_it2.3014.51688
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 82 -
Rwork0.235 1704 -
all-1786 -
obs--99.89 %
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)
11.21780.2379-0.11550.67640.08851.3672-0.03790.0825-0.0420.04460.057-0.0821-0.06840.0193-0.01910.01990.0105-0.01060.083-0.01240.02095.42455.03515.543
20.96270.11960.05332.3451-0.98762.8892-0.02410.05880.0405-0.3390.1020.23360.1572-0.0398-0.07780.1082-0.022-0.02810.02370.00920.0250.84443.90362.123
31.7013-0.2514-0.18541.742-0.42260.4743-0.0334-0.103-0.06950.12370.0140.0873-0.01090.05540.01940.0570.00630.02390.02930.010.0148-1.04138.06887.704
40.9610.6784-0.59362.9602-2.19112.9056-0.130.0885-0.0613-0.55680.16950.0520.5345-0.0913-0.03940.194-0.0066-0.01090.0389-0.02160.02813.98438.72760.862
53.2864-1.07030.97592.5630.10476.37790.0943-0.3144-0.36230.1099-0.03760.28690.8345-0.2792-0.05680.1258-0.02610.01250.06840.04020.0643-5.97442.39432.436
61.94510.1473-0.26590.46240.04430.90590.00720.02450.0840.05550.02860.00270.01870.0108-0.03580.01930.01210.00640.0312-0.00090.0361-21.61956.74116.588
70.5627-0.4202-0.20990.36040.17550.44960.02970.02640.05740.0177-0.0064-0.0127-0.0351-0.0282-0.02320.05270.0170.01080.03230.00380.0542-41.10564.76426.015
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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