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- PDB-1h9t: FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN ... -

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Basic information

Entry
Database: PDB / ID: 1h9t
TitleFADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR
Components
  • 5'-D(*CP*AP*TP*CP*TP*GP*GP*TP*AP*CP*GP*AP* CP*CP*AP*GP*AP*TP*C)-3'
  • 5'-D(*GP*AP*TP*CP*TP*GP*GP*TP*CP*GP*TP*AP* CP*CP*AP*GP*AP*TP*G)-3'
  • FATTY 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 / 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 / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsVan Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J.
Citation
Journal: Embo J. / Year: 2001
Title: The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr
Authors: Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J.
#1: 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. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
#2: 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
DepositionMar 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID METABOLISM REGULATOR PROTEIN
B: FATTY ACID METABOLISM REGULATOR PROTEIN
X: 5'-D(*CP*AP*TP*CP*TP*GP*GP*TP*AP*CP*GP*AP* CP*CP*AP*GP*AP*TP*C)-3'
Y: 5'-D(*GP*AP*TP*CP*TP*GP*GP*TP*CP*GP*TP*AP* CP*CP*AP*GP*AP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1379
Polymers66,6374
Non-polymers5005
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.992, 92.992, 334.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99886, -0.0443, -0.00809), (-0.04385, 0.93788, 0.34586), (-0.00768, 0.34511, -0.93803)
Vector: -9.641, -54.392, 303.78799)
DetailsPROTEIN AND THE TWO DNA CHAINS

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FATTY ACID METABOLISM REGULATOR PROTEIN


Mass: 27493.111 Da / Num. of mol.: 2
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

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DNA chain , 2 types, 2 molecules XY

#2: DNA chain 5'-D(*CP*AP*TP*CP*TP*GP*GP*TP*AP*CP*GP*AP* CP*CP*AP*GP*AP*TP*C)-3'


Mass: 5789.762 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*GP*AP*TP*CP*TP*GP*GP*TP*CP*GP*TP*AP* CP*CP*AP*GP*AP*TP*G)-3'


Mass: 5860.796 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 30 molecules

#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 60.77 %
Crystal growpH: 6.5 / Details: SODIUM CITRATE PH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14.6 mg/mlprotein1drop
250 mM1dropKH2PO4
310 %glycerol1drop
4200 mMmagnesium acetate1reservoir
5100 mMsodium cacodylate1reservoir
6myristoyl-CoA1drop2-fold molar excess

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.02467
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02467 Å / Relative weight: 1
ReflectionResolution: 3.25→25 Å / Num. obs: 88082 / % possible obs: 98 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.6
Reflection shellResolution: 3.25→3.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 14138 / Num. measured all: 88082
Reflection shell
*PLUS
% possible obs: 98.6 % / Redundancy: 4.5 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2X

1e2x


Resolution: 3.25→12 Å / SU B: 32 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0
RfactorNum. reflection% reflectionSelection details
Rfree0.32 391 2.8 %RANDOM
Rwork0.264 ---
obs0.265 13374 98.09 %-
Displacement parametersBiso mean: 66.611 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å22.68 Å20 Å2
2--5.37 Å20 Å2
3----8.05 Å2
Refinement stepCycle: LAST / Resolution: 3.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 773 5 25 4434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.7
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.351.5
X-RAY DIFFRACTIONp_mcangle_it2.052
X-RAY DIFFRACTIONp_scbond_it2.222
X-RAY DIFFRACTIONp_scangle_it3.312.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.32
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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