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- PDB-6o6p: Structure of the regulator FasR from Mycobacterium tuberculosis i... -

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Basic information

Entry
Database: PDB / ID: 6o6p
TitleStructure of the regulator FasR from Mycobacterium tuberculosis in complex with DNA
Components
  • DNA-forward
  • DNA-reverse
  • TetR family transcriptional regulator
KeywordsTRANSCRIPTION/DNA / TetR-like transcription factor / fatty acid biosynthesis regulation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Tetracyclin repressor-like MT0489/Rv0472c, C-terminal domain / 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
DNA / DNA (> 10) / Probable transcriptional regulatory protein (Probably TetR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.851 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: DNA-forward
D: DNA-reverse


Theoretical massNumber of molelcules
Total (without water)69,9314
Polymers69,9314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.697, 174.680, 158.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 38 through 77 or (resid 78...
21(chain B and (resid 38 through 90 or (resid 91...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYR(chain A and (resid 38 through 77 or (resid 78...AA38 - 7758 - 97
12GLNGLNGLNGLN(chain A and (resid 38 through 77 or (resid 78...AA7898
13ARGARGPROPRO(chain A and (resid 38 through 77 or (resid 78...AA37 - 22457 - 244
14ARGARGPROPRO(chain A and (resid 38 through 77 or (resid 78...AA37 - 22457 - 244
15ARGARGPROPRO(chain A and (resid 38 through 77 or (resid 78...AA37 - 22457 - 244
16ARGARGPROPRO(chain A and (resid 38 through 77 or (resid 78...AA37 - 22457 - 244
21ASPASPVALVAL(chain B and (resid 38 through 90 or (resid 91...BB38 - 9058 - 110
22LEULEULEULEU(chain B and (resid 38 through 90 or (resid 91...BB91111
23ASPASPPROPRO(chain B and (resid 38 through 90 or (resid 91...BB38 - 22458 - 244
24ASPASPPROPRO(chain B and (resid 38 through 90 or (resid 91...BB38 - 22458 - 244
25ASPASPPROPRO(chain B and (resid 38 through 90 or (resid 91...BB38 - 22458 - 244
26ASPASPPROPRO(chain B and (resid 38 through 90 or (resid 91...BB38 - 22458 - 244

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Components

#1: Protein TetR family transcriptional regulator


Mass: 27286.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3208 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O05858
#2: DNA chain DNA-forward


Mass: 7627.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: DNA chain DNA-reverse


Mass: 7729.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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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: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG2000 MME, 0.25 M ammonium citrate, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.85→39.54 Å / Num. obs: 6467 / % possible obs: 76.5 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.055 / Rrim(I) all: 0.176 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.85-4.315.61.45414520.6230.5951.58162.3
8.61-39.54110.0638210.9980.020.06699

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Processing

Software
NameClassification
PHENIXrefinement
Aimlessdata scaling
TRUNCATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O6N

6o6n


Resolution: 3.851→39.066 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.78
RfactorNum. reflection% reflection
Rfree0.3315 647 10.06 %
Rwork0.2875 --
obs0.2919 6431 76.42 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 357.1 Å2 / Biso mean: 155.8803 Å2 / Biso min: 49.58 Å2
Refinement stepCycle: final / Resolution: 3.851→39.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 943 0 0 3803
Num. residues----421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1532X-RAY DIFFRACTION11.988TORSIONAL
12B1532X-RAY DIFFRACTION11.988TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8509-4.14790.42641020.396488999161
4.1479-4.56480.34791110.35591017112868
4.5648-5.22390.37661070.32651114122173
5.2239-6.57650.34921510.34321256140783
6.5765-39.06840.29991760.23031508168495
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)
14.0381-0.6395-3.31127.7227-3.63239.58950.5665-0.4276-0.04040.00960.18881.1421-2.34580.4999-0.60781.44260.28290.10941.5383-0.19241.2964-17.941721.873836.3593
26.68776.8583-2.3088.7598-3.37672.64190.4081-2.8260.87871.7593-0.99470.1154-1.95880.13380.31091.68640.1470.01222.0886-0.23321.0371-3.315142.337825.0672
34.63243.80390.63952.0419-2.24375.6825-1.5222-0.19490.1231-1.76070.67111.98572.42161.6344-0.16730.91390.4550.48080.9932-0.05171.4866-13.984615.60242.6139
44.43273.80970.60766.31831.06282.7757-0.3308-0.26440.0344-0.5002-0.2349-0.8834-0.30360.12660.59041.64130.24510.03560.93760.16251.21273.916534.69899.4298
51.9087-4.0667-0.78324.4213.76312.0939-0.2139-0.3263-0.68022.2373-0.3410.5524.8531-2.59310.36951.4785-0.60760.43161.3920.26040.9202-28.01656.471825.5227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 37:81A37 - 81
2X-RAY DIFFRACTION2chain A and resid 82:224A82 - 224
3X-RAY DIFFRACTION3chain B and resid 38:81B38 - 81
4X-RAY DIFFRACTION4chain B and resid 82:224B82 - 224
5X-RAY DIFFRACTION5chain C or chain DC3 - 25
6X-RAY DIFFRACTION5chain C or chain DD1 - 23

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