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- PDB-6o6n: Structure of the regulator FasR from Mycobacterium tuberculosis i... -

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Basic information

Entry
Database: PDB / ID: 6o6n
TitleStructure of the regulator FasR from Mycobacterium tuberculosis in complex with C20-CoA
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / TetR-like transcription factor / fatty acid biosynthesis regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Arachinoyl-CoA / HTH-type transcriptional repressor KstR2 / HTH-type transcriptional activator FasR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.7 Å
AuthorsLarrieux, N. / Trajtenberg, F. / Lara, J. / Gramajo, H. / Buschiazzo, A.
CitationJournal: Nat Commun / Year: 2020
Title: Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine.
Authors: Lara, J. / Diacovich, L. / Trajtenberg, F. / Larrieux, N. / Malchiodi, E.L. / Fernandez, M.M. / Gago, G. / Gramajo, H. / Buschiazzo, A.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 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: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7254
Polymers21,5921
Non-polymers1,1333
Water3,891216
1
A: TetR family transcriptional regulator
hetero molecules

A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4518
Polymers43,1852
Non-polymers2,2666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4000 Å2
ΔGint-69 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.146, 108.146, 43.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21A-570-

HOH

31A-571-

HOH

41A-608-

HOH

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Components

#1: Protein TetR family transcriptional regulator / TetR/AcrR family transcriptional regulator / FasR


Mass: 21592.369 Da / Num. of mol.: 1 / Fragment: delta-33 construct (UNP residues 35-225)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: kstR2_2, kstR2_1, kstR2_3, kstR2_4, kstR2_5, kstR2_6, kstR2_7, DSI35_30495, ERS007661_03222, ERS007663_03464, ERS007665_00400, ERS007720_01056, ERS007741_00500, ERS023446_00266, ERS027646_ ...Gene: kstR2_2, kstR2_1, kstR2_3, kstR2_4, kstR2_5, kstR2_6, kstR2_7, DSI35_30495, ERS007661_03222, ERS007663_03464, ERS007665_00400, ERS007720_01056, ERS007741_00500, ERS023446_00266, ERS027646_02562, ERS027651_00856, ERS027652_02035, ERS027653_03199, ERS027656_00595, ERS027666_01457, ERS124361_00903, SAMEA2682864_03848, SAMEA2683035_03897
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045JBR0, UniProt: O05858*PLUS
#2: Chemical ChemComp-5F9 / Arachinoyl-CoA


Mass: 1062.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H74N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 2.2 M sodium chloride, 0.1 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→20.2 Å / Num. obs: 28969 / % possible obs: 99.8 % / Redundancy: 14.181 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.067 / Χ2: 1.132 / Net I/σ(I): 22.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.813.9211.4681.645630.7141.52398.8
1.8-1.9314.7830.8023.1743210.8940.83100
1.93-2.0814.3020.4066.5440680.9730.421100
2.08-2.2814.4450.19114.1337260.9940.198100
2.28-2.5514.3490.11323.5233990.9970.117100
2.55-2.9414.4090.06737.1530360.9990.069100
2.94-3.5913.9740.04852.3125820.9990.05100
3.59-5.0713.3860.03569.0920450.9990.037100
5.07-20.212.5450.02768.9122910.02899.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.7→20.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1379 4.99 %RANDOM
Rwork0.181 ---
obs0.182 27645 95.5 %-
Displacement parametersBiso max: 108.12 Å2 / Biso mean: 25.3 Å2 / Biso min: 3.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.1602 Å20 Å20 Å2
2---0.1602 Å20 Å2
3---0.3204 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.7→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 36 217 1773
Biso mean--36.77 37.91 -
Num. residues----195
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d573SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes285HARMONIC5
X-RAY DIFFRACTIONt_it1610HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion199SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2224SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1610HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2182HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion14.04
LS refinement shellResolution: 1.7→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2509 35 6.33 %
Rwork0.2013 518 -
all0.2039 553 -
obs--91.83 %
Refinement TLS params.Method: refined / Origin x: 20.09 Å / Origin y: -29.0942 Å / Origin z: 2.817 Å
111213212223313233
T-0.0304 Å2-0.0104 Å20.0016 Å2--0.0214 Å2-0.0052 Å2---0.0164 Å2
L0.6559 °2-0.0969 °2-0.0921 °2-0.2161 °20.233 °2--0.4958 °2
S-0.0024 Å °-0.0489 Å °0.0302 Å °-0.0157 Å °-0.0092 Å °0.0732 Å °0.0439 Å °-0.0481 Å °0.0116 Å °
Refinement TLS groupSelection details: { A|* }

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