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- PDB-6o6o: Structure of the regulator FasR from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6o6o
TitleStructure of the regulator FasR from Mycobacterium tuberculosis
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
MYRISTIC ACID / HTH-type transcriptional repressor KstR2 / HTH-type transcriptional activator FasR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: TetR family transcriptional regulator
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6414
Polymers43,1852
Non-polymers4572
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.130, 100.180, 38.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-451-

HOH

21B-463-

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.: 2 / 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
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045JBR0, UniProt: O05858*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 22% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2016 / Details: Varimax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.63→28.78 Å / Num. obs: 41807 / % possible obs: 98.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 11.3 / Num. measured all: 147330 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.63-1.663.50.467700519990.7980.2840.5491.896.4
8.93-28.7830.0269273130.9970.0180.03224.797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O6N

6o6n


Resolution: 1.63→28.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1692 4.05 %RANDOM
Rwork0.219 ---
obs0.219 41762 98.3 %-
Displacement parametersBiso max: 117.21 Å2 / Biso mean: 36.18 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.7664 Å20 Å20 Å2
2--2.8423 Å20 Å2
3----2.0759 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.63→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 32 205 3128
Biso mean--43.54 41.56 -
Num. residues----374
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1091SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes559HARMONIC5
X-RAY DIFFRACTIONt_it3120HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion390SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies15HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4119SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3120HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4248HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion17.5
LS refinement shellResolution: 1.63→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.238 46 5.5 %
Rwork0.247 790 -
all0.2465 836 -
obs--96.45 %
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)
11.2628-0.87140.19850.8822-0.14560.2006-0.1797-0.1718-0.2370.21830.13170.1593-0.0303-0.09120.048-0.0130.0090.0539-0.04620.0124-0.029931.331199.507438.8083
20.9415-0.0680.42521.1160.11360.6325-0.00710.019-0.1475-0.06310.0310.21870.03550.0006-0.0239-0.05270.01750.0109-0.037-0.0235-0.046912.3638102.35721.7906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A35 - 224
2X-RAY DIFFRACTION2{ B|* }B40 - 225

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