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- PDB-1hw1: THE FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METAB... -

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Basic information

Entry
Database: PDB / ID: 1hw1
TitleTHE FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ESCHERICHIA COLI
ComponentsFATTY ACID METABOLISM REGULATOR PROTEIN
KeywordsTRANSCRIPTION / helix-turn-helix / helix bundle
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
Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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 24, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6479
Polymers54,0052
Non-polymers6427
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-123 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.346, 86.996, 59.128
Angle α, β, γ (deg.)90.00, 120.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5.6
Details: ammonium sulfate, lithium sulfate, sodium citrate, zinc chloride, pH 5.6, EVAPORATION, temperature 290.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium citrate1reservoirpH5.6
30.7 Mammonium sulfate1reservoir
40.2 Mlithium sulfate1reservoir
55 mMzinc chloride1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD / Date: Sep 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 1306223 / Num. obs: 80658 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.8
Reflection
*PLUS
Num. measured all: 1306223
Reflection shell
*PLUS
% possible obs: 78.9 % / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3974 -RANDOM
Rwork0.198 ---
all-78944 --
obs-74970 95.2 %-
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.075 Å20 Å20.201 Å2
2---0.234 Å20 Å2
3---2.309 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 31 416 4043
LS refinement shellResolution: 1.5→1.55 Å
RfactorNum. reflection% reflection
Rfree0.2629 299 -
Rwork0.2255 --
obs-5851 78.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.109
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.994
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.806
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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