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- PDB-1e2x: FadR, fatty acid responsive transcription factor from E. coli -

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Basic information

Entry
Database: PDB / ID: 1e2x
TitleFadR, fatty acid responsive transcription factor from E. coli
ComponentsFATTY ACID METABOLISM REGULATOR PROTEIN
KeywordsTRANSCRIPTIONAL REGULATION
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 / GntR ligand-binding domain-like / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / GntR ligand-binding domain-like / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fatty acid metabolism regulator protein / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVan Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
Citation
Journal: Embo J. / Year: 2000
Title: Crystal Structure of Fadr, a Fatty Acid-Responsive Transcription Factor with a Novel Acyl Coenzyme A-Binding Fold
Authors: Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and X-Ray Diffraction Studies of the Fatty-Acid Responsive Transcription Factor Fadr from Escherichia Coli.
Authors: Van Aalten, D.M.F. / Knudsen, J. / Dirusso, C.C. / Kokko, T. / Wierenga, R.K.
History
DepositionMay 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6853
Polymers27,4931
Non-polymers1922
Water2,810156
1
A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules

A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3706
Polymers54,9862
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)59.711, 101.973, 87.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4002-

SO4

21A-2045-

HOH

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Components

#1: Protein FATTY ACID METABOLISM REGULATOR PROTEIN


Mass: 27493.111 Da / Num. of mol.: 1 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09371, UniProt: P0A8V6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.48 Å3/Da / Density % sol: 50.05 %
Crystal growpH: 9 / Details: LI2SO4/(NH4)2SO4, TRIS PH 9
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.6 mg/mlprotein1drop
250 mM1dropKH2PO4
310 %glycerol1drop
42.3 Mammonium sulfate1reservoir
50.75 M1reservoirLiSO4
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535, 1.0
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95351
211
ReflectionResolution: 2→25 Å / Num. obs: 18125 / % possible obs: 95.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.6 / % possible all: 74
Reflection shell
*PLUS
% possible obs: 73.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.48 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1880425.42 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME RESIDUES TRUNCATED TO ALA OR GLY DUE TO POORLY DEFINED ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 744 4.1 %RANDOM
Rwork0.2 ---
obs0.2 17945 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9511 Å2 / ksol: 0.35566 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å20 Å2
2---8.58 Å20 Å2
3---3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 10 156 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 110 3.9 %
Rwork0.27 2741 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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