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- PDB-1hw2: FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLIS... -

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Basic information

Entry
Database: PDB / ID: 1hw2
TitleFADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ECHERICHIA COLI
Components
  • 5'-D(*CP*GP*AP*TP*CP*TP*GP*GP*TP*CP*CP*GP*AP*CP*CP*AP*GP*AP*TP*GP*CP*T)-3'
  • 5'-D(*G*CP*AP*TP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*CP*AP*GP*AP*TP*CP*GP*A)-3'
  • FATTY ACID METABOLISM REGULATOR PROTEIN
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / helix bundle / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
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 / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / 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 / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / 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
DNA / DNA (> 10) / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsXu, Y. / Heath, R.J. / Li, Z. / Rock, C.O. / White, S.W.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli.
Authors: Xu, Y. / Heath, R.J. / Li, Z. / Rock, C.O. / White, S.W.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*CP*GP*AP*TP*CP*TP*GP*GP*TP*CP*CP*GP*AP*CP*CP*AP*GP*AP*TP*GP*CP*T)-3'
E: 5'-D(*G*CP*AP*TP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*CP*AP*GP*AP*TP*CP*GP*A)-3'
A: FATTY ACID METABOLISM REGULATOR PROTEIN
B: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5355
Polymers67,5114
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.733, 110.148, 130.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*CP*GP*AP*TP*CP*TP*GP*GP*TP*CP*CP*GP*AP*CP*CP*AP*GP*AP*TP*GP*CP*T)-3'


Mass: 6728.341 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*G*CP*AP*TP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*CP*AP*GP*AP*TP*CP*GP*A)-3'


Mass: 6777.379 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein FATTY ACID METABOLISM REGULATOR PROTEIN / FADR


Mass: 27002.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FADR / Plasmid: PPJ139 / Production host: Escherichia coli (E. coli) / Strain (production host): UB1005 / References: UniProt: P0A8V6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 4.41 Å3/Da / Density % sol: 72.12 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6
Details: isopropanol, MES, magnesium chloride, pH 6.0, EVAPORATION, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1isopropanol11
2MES11
3MgCl211
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
210 %isopropyl alcohol1reservoir
350 mMMES1reservoirpH6.0
410 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorDetector: CCD / Date: Sep 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 643902 / Num. obs: 20310 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.7
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.346 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 643902
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native FadR dimer

Resolution: 3.25→40 Å / Isotropic thermal model: grouped-B / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 898 random
Rwork0.235 --
all-18568 -
obs-17670 -
Displacement parametersBiso mean: 70.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.667 Å20 Å20 Å2
2---8.077 Å20 Å2
3---14.745 Å2
Refinement stepCycle: LAST / Resolution: 3.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 773 1 0 4294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d1.7
LS refinement shellResolution: 3.25→3.37 Å
RfactorNum. reflection% reflection
Rfree0.358 74 -
Rwork0.3037 --
obs--83.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 70.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.358

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