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- PDB-5dv5: The fatty acid-responsive FadR repressor of Vibrio alginolyticus ... -

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Basic information

Entry
Database: PDB / ID: 5dv5
TitleThe fatty acid-responsive FadR repressor of Vibrio alginolyticus complex with Palmitoyl-CoA
ComponentsGntR family transcriptional regulator
KeywordsTRANSCRIPTION / fatty acid-responsive FadR repressor / palmitoyl1-CoA ester binding / DNA binding
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Palmitoyl-CoA / :
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLin, Y. / Li, D.F. / Feng, Y.J.
CitationJournal: To Be Published
Title: Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing
Authors: Feng, Y.J. / Lin, Y. / Li, D.F. / Zhang, H.M. / Gao, R.S. / Bi, L.J. / Wang, S.H.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GntR family transcriptional regulator
B: GntR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8346
Polymers68,8102
Non-polymers4,0244
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-25 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 88.480, 61.650
Angle α, β, γ (deg.)90.00, 93.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GntR family transcriptional regulator


Mass: 34405.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Strain: E0666 / Gene: AAW52_18775 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0G9LXQ8
#2: Chemical
ChemComp-PKZ / Palmitoyl-CoA


Mass: 1005.943 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H66N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 4% Tacsimate pH 5.0, 11% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→61.56 Å / Num. obs: 20475 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.7 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DV1

5dv1
PDB Unreleased entry


Resolution: 2.4→45.278 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 2021 9.88 %Random
Rwork0.1905 ---
obs0.1962 20456 92.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 260 87 4675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024688
X-RAY DIFFRACTIONf_angle_d0.6776344
X-RAY DIFFRACTIONf_dihedral_angle_d14.4471762
X-RAY DIFFRACTIONf_chiral_restr0.027672
X-RAY DIFFRACTIONf_plane_restr0.002786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.46010.33481250.24351180X-RAY DIFFRACTION84
2.4601-2.52660.30461320.23091190X-RAY DIFFRACTION83
2.5266-2.60090.26361230.22391193X-RAY DIFFRACTION85
2.6009-2.68490.27261420.22231192X-RAY DIFFRACTION84
2.6849-2.78080.31591280.22591254X-RAY DIFFRACTION87
2.7808-2.89210.28141310.22211281X-RAY DIFFRACTION91
2.8921-3.02370.27491580.22361340X-RAY DIFFRACTION94
3.0237-3.18310.27081530.21621358X-RAY DIFFRACTION96
3.1831-3.38250.24041540.2091392X-RAY DIFFRACTION97
3.3825-3.64360.25121500.1891399X-RAY DIFFRACTION98
3.6436-4.010.25481590.18381398X-RAY DIFFRACTION98
4.01-4.58980.22891470.16221393X-RAY DIFFRACTION98
4.5898-5.78080.22961570.17161427X-RAY DIFFRACTION98
5.7808-45.28610.19881620.15991438X-RAY DIFFRACTION98

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