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- PDB-4p9u: FadR, Fatty Acid Responsive Transcription Factor from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 4p9u
TitleFadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with DNA
Components
  • (DNA (31-MER)) x 2
  • Fatty acid metabolism regulator protein
KeywordsTranscription Regulator/DNA / transcription regulator / protein-DNA complex / Transcription Regulator-DNA complex
Function / homology
Function and homology information


negative regulation of phospholipid biosynthetic process / fatty-acyl-CoA binding / regulation of fatty acid metabolic process / fatty acid metabolic process / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.208 Å
AuthorsKull, F.J. / Shi, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072661 United States
CitationJournal: Nat Commun / Year: 2015
Title: The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
Authors: Shi, W. / Kovacikova, G. / Lin, W. / Taylor, R.K. / Skorupski, K. / Kull, F.J.
History
DepositionApr 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Fatty acid metabolism regulator protein
F: Fatty acid metabolism regulator protein
G: DNA (31-MER)
H: DNA (31-MER)
A: Fatty acid metabolism regulator protein
B: Fatty acid metabolism regulator protein
C: DNA (31-MER)
D: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)163,2138
Polymers163,2138
Non-polymers00
Water00
1
E: Fatty acid metabolism regulator protein
F: Fatty acid metabolism regulator protein
G: DNA (31-MER)
H: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)81,6074
Polymers81,6074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-44 kcal/mol
Surface area34630 Å2
MethodPISA
2
A: Fatty acid metabolism regulator protein
B: Fatty acid metabolism regulator protein
C: DNA (31-MER)
D: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)81,6074
Polymers81,6074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-45 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.600, 94.700, 101.700
Angle α, β, γ (deg.)89.800, 114.600, 116.500
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Fatty acid metabolism regulator protein


Mass: 31272.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: fadR, VC_1900 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQU8
#2: DNA chain DNA (31-MER)


Mass: 9531.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (31-MER)


Mass: 9530.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)

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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: 3.89 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M TRIS pH 8.5, 1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 21, 2013
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3.208→19.89 Å / Num. obs: 40186 / % possible obs: 98.42 % / Redundancy: 3.51 % / Biso Wilson estimate: 65.11 Å2 / Net I/σ(I): 12.97
Reflection shellResolution: 3.208→3.322 Å / Mean I/σ(I) obs: 3 / % possible all: 95.86

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER(phenix.molecular replacement: 1.8.4_1496)phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P96

4p96


Resolution: 3.208→19.888 Å / FOM work R set: 0.814 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2.15 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1990 4.97 %Random selection
Rwork0.2176 38051 --
obs0.2193 40186 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.63 Å2 / Biso mean: 87.02 Å2 / Biso min: 33.12 Å2
Refinement stepCycle: final / Resolution: 3.208→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8804 2542 0 0 11346
Num. residues----1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711848
X-RAY DIFFRACTIONf_angle_d1.35716550
X-RAY DIFFRACTIONf_chiral_restr0.0551816
X-RAY DIFFRACTIONf_plane_restr0.0071696
X-RAY DIFFRACTIONf_dihedral_angle_d20.9274600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2079-3.28780.33421320.32752508264091
3.2878-3.37630.35641430.29642750289397
3.3763-3.47510.35251420.26642727286998
3.4751-3.58660.31721390.26762692283198
3.5866-3.7140.26551410.25182713285498
3.714-3.86170.27381440.22622759290399
3.8617-4.03610.30771450.23012719286498
4.0361-4.24690.27051430.21292770291399
4.2469-4.51010.21941390.20122724286399
4.5101-4.85360.2711460.19182712285899
4.8536-5.33350.23141470.21532767291499
5.3335-6.08580.24561430.22392719286299
6.0858-7.59580.24181380.2112753289199
7.5958-19.88790.15941480.15892738288698

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