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- PDB-8y3z: VcFadRqm, Genetically engineered mutants of Vibrio cholerae fadR,... -

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Basic information

Entry
Database: PDB / ID: 8y3z
TitleVcFadRqm, Genetically engineered mutants of Vibrio cholerae fadR, in Complex with DNA
Components
  • (DNA (31-MER)) x 2
  • Fatty acid metabolism regulator protein
KeywordsDNA BINDING PROTEIN / Complex
Function / homology
Function and homology information


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 / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTsui, W. / Shi, W. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The unexpected conformational and functional change upon disruption of the additional fatty acyl-CoA ligand binding in Vibrio cholerae FadR
Authors: Tsui, W. / Shi, W.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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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
C: DNA (31-MER)
D: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3687
Polymers83,0864
Non-polymers2823
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.303, 99.303, 225.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fatty acid metabolism regulator protein


Mass: 32010.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: fadR, BC353_03540, D6U24_01375, ERS013165_00302, ERS013186_01100, ERS013201_00358, EYB64_05555, F0H40_07700, F0M16_02315, FLM02_10025, FLM12_09940, I7465_02975
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A085QQF2

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (31-MER)


Mass: 9448.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (31-MER)


Mass: 9617.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)

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Non-polymers , 3 types, 44 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 289.15 K / Method: in cell / pH: 7.5 / Details: 16%(w/v)PEG8000,40mM KH2PO4,20%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 39938 / % possible obs: 99.9 % / Redundancy: 2.52 % / Biso Wilson estimate: 71.85 Å2 / Rmerge(I) obs: 0.0117 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 35669 / CC1/2: 0.01 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.81 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 2047 5.13 %RANDOM
Rwork0.2345 ---
obs0.2349 39938 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 1265 16 41 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095921
X-RAY DIFFRACTIONf_angle_d1.1968276
X-RAY DIFFRACTIONf_dihedral_angle_d25.8082282
X-RAY DIFFRACTIONf_chiral_restr0.095901
X-RAY DIFFRACTIONf_plane_restr0.008853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35411250.36532509X-RAY DIFFRACTION100
2.56-2.620.41271430.34692458X-RAY DIFFRACTION100
2.62-2.690.36161240.33522499X-RAY DIFFRACTION100
2.69-2.770.2981290.32192479X-RAY DIFFRACTION100
2.77-2.860.3451450.31342476X-RAY DIFFRACTION100
2.86-2.960.34541320.3042485X-RAY DIFFRACTION100
2.96-3.080.33631370.31862499X-RAY DIFFRACTION100
3.08-3.220.32351510.3082479X-RAY DIFFRACTION100
3.22-3.390.30051500.29352467X-RAY DIFFRACTION100
3.39-3.60.26651270.2712526X-RAY DIFFRACTION100
3.6-3.880.27661320.24692530X-RAY DIFFRACTION100
3.88-4.270.22281270.21252560X-RAY DIFFRACTION100
4.27-4.890.18491420.19082551X-RAY DIFFRACTION100
4.89-6.150.20251490.20822605X-RAY DIFFRACTION100
6.15-29.810.18071340.17992768X-RAY DIFFRACTION100

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