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

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Basic information

Entry
Database: PDB / ID: 4pdk
TitleFadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with oleoyl-CoA
ComponentsFatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / transcription regulator
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
Chem-3VV / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsShi, W. / Kull, F.J.
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 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: 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
B: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1976
Polymers64,0692
Non-polymers4,1284
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-17 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.920, 88.690, 62.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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Components

#1: Protein Fatty acid metabolism regulator protein


Mass: 32034.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fadR, VC_1900 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQU8
#2: Chemical
ChemComp-3VV / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) / oleoyl-CoA


Mass: 1031.980 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H68N7O17P3S

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3350, 0.23M magnesium formate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→19.73 Å / Num. obs: 16577 / % possible obs: 99.3 % / Redundancy: 3.63 % / Biso Wilson estimate: 35.03 Å2 / Net I/σ(I): 11.48

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASER(phenix.molecular replacement: 1.8.4_1496)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.73 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2982 1654 9.99 %
Rwork0.2585 14904 -
obs0.2628 16558 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.3 Å2 / Biso mean: 73.2325 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: final / Resolution: 2.8→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 268 0 4508
Biso mean--59.13 --
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014610
X-RAY DIFFRACTIONf_angle_d2.1486236
X-RAY DIFFRACTIONf_chiral_restr0.095656
X-RAY DIFFRACTIONf_plane_restr0.009774
X-RAY DIFFRACTIONf_dihedral_angle_d22.5281724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2211X-RAY DIFFRACTION14.043TORSIONAL
12B2211X-RAY DIFFRACTION14.043TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.88220.41350.3611226136199
2.8822-2.97490.35041350.31681203133899
2.9749-3.08080.35041340.322712221356100
3.0808-3.20370.39321350.30351213134899
3.2037-3.34880.30351360.28971224136099
3.3488-3.52440.30681370.271212351372100
3.5244-3.74380.30111380.257412351373100
3.7438-4.03060.26571370.250512451382100
4.0306-4.43210.27361380.226312441382100
4.4321-5.0640.29211380.213412481386100
5.064-6.34470.28621440.243412861430100
6.3447-19.730.23641470.21721323147099
Refinement TLS params.Method: refined / Origin x: 16.9316 Å / Origin y: -20.042 Å / Origin z: -9.1424 Å
111213212223313233
T0.0825 Å2-0.0277 Å20.0138 Å2--0.0094 Å20.0526 Å2---0.0459 Å2
L0.0024 °20.0125 °20.0099 °2-0.0093 °2-0.0109 °2--0.0189 °2
S-0.055 Å °-0.0149 Å °-0.0786 Å °-0.0185 Å °-0.0372 Å °0.0702 Å °0.0071 Å °-0.0537 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 266
2X-RAY DIFFRACTION1allA1267 - 1268
3X-RAY DIFFRACTION1allB8 - 1268

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