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- PDB-9wfi: A chimera FadR transcription factor containing wHTH of Rv0494 and... -

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Basic information

Entry
Database: PDB / ID: 9wfi
TitleA chimera FadR transcription factor containing wHTH of Rv0494 and the part other than wHTH of Escherichia coli FadR
ComponentsUncharacterized HTH-type transcriptional regulator Rv0494,Fatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


fatty-acyl-CoA binding / regulation of fatty acid metabolic process / positive regulation of fatty acid biosynthetic process / fatty acid metabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol
Similarity search - Function
Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Fatty acid metabolism regulator protein / Uncharacterized HTH-type transcriptional regulator Rv0494
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLu, L.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32460022 China
CitationJournal: To Be Published
Title: A chimera FadR transcription factor containing wHTH of Rv0494 and the part other than wHTH of Escherichia coli FadR
Authors: Lu, L.N.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator Rv0494,Fatty acid metabolism regulator protein
B: Uncharacterized HTH-type transcriptional regulator Rv0494,Fatty acid metabolism regulator protein


Theoretical massNumber of molelcules
Total (without water)55,9352
Polymers55,9352
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-19 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.678, 66.136, 122.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator Rv0494,Fatty acid metabolism regulator protein


Mass: 27967.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: M1-S80 is the wHTH of Rv0494 wHTH; K81-R250 is the part other than wHTH of Escherichia coli FadR.,M1-S80 is the wHTH of Rv0494 wHTH; K81-R250 is the part other than wHTH of Escherichia coli FadR.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: Rv0494, MTCY20G9.20, fadR, oleR, thdB, b1187, JW1176 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMG7, UniProt: P0A8V6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→35.64 Å / Num. obs: 46377 / % possible obs: 97.88 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.997 / Net I/σ(I): 2.11
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 4673 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→35.64 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 1999 4.33 %
Rwork0.2119 44192 -
obs0.2134 46191 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 0 249 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593551
X-RAY DIFFRACTIONf_angle_d0.78744811
X-RAY DIFFRACTIONf_chiral_restr0.0477534
X-RAY DIFFRACTIONf_plane_restr0.0081635
X-RAY DIFFRACTIONf_dihedral_angle_d4.8825489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.40071450.36643195X-RAY DIFFRACTION97.75
1.79-1.840.35541440.3223205X-RAY DIFFRACTION97.72
1.84-1.90.36781470.29673231X-RAY DIFFRACTION98
1.9-1.960.32851160.27342601X-RAY DIFFRACTION78.82
1.96-2.030.27461460.22893208X-RAY DIFFRACTION98.42
2.03-2.110.24221470.21433254X-RAY DIFFRACTION98.58
2.11-2.20.24541470.20143266X-RAY DIFFRACTION98.67
2.2-2.320.27411000.19852178X-RAY DIFFRACTION66.2
2.32-2.470.24611480.20793280X-RAY DIFFRACTION98.53
2.47-2.660.24181490.2113292X-RAY DIFFRACTION99.16
2.66-2.920.25011490.20733303X-RAY DIFFRACTION99.08
2.92-3.350.23051500.20463315X-RAY DIFFRACTION98.69
3.35-4.210.22531530.19483371X-RAY DIFFRACTION98.91
4.22-35.640.21821580.19293493X-RAY DIFFRACTION98.68

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