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- PDB-8ivi: crystal structure of a medium-long chain fatty acyl-CoA ligase -

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Basic information

Entry
Database: PDB / ID: 8ivi
Titlecrystal structure of a medium-long chain fatty acyl-CoA ligase
ComponentsMedium/long-chain-fatty-acid--CoA ligase FadD8
KeywordsLIGASE / fatty acyl-CoA / mycobacterial protein
Function / homology
Function and homology information


medium-chain acyl-CoA ligase / long-chain-fatty-acid-CoA ligase / long-chain fatty acid-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / ATP binding / plasma membrane
Similarity search - Function
: / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Medium/long-chain-fatty-acid--CoA ligase FadD8
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLi, S.
Funding support China, 1items
OrganizationGrant numberCountry
Health Commission of Henan ProvinceLHGJ20190242 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural study of medium-long chain fatty acyl-CoA ligase FadD8 from Mycobacterium tuberculosis.
Authors: Li, S. / Qu, Y.
History
DepositionMar 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Medium/long-chain-fatty-acid--CoA ligase FadD8
B: Medium/long-chain-fatty-acid--CoA ligase FadD8


Theoretical massNumber of molelcules
Total (without water)126,6082
Polymers126,6082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-5 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.230, 105.000, 135.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Medium/long-chain-fatty-acid--CoA ligase FadD8 / FACL8


Mass: 63304.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: fadD8, Rv0551c / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06417, medium-chain acyl-CoA ligase, long-chain-fatty-acid-CoA ligase

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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: 1.86 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→66.24 Å / Num. obs: 81612 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.6
Reflection shellResolution: 2.29→2.35 Å / Rmerge(I) obs: 0.825 / Num. unique obs: 3149

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→52.5 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 3778 4.63 %
Rwork0.2466 --
obs0.2479 81612 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→52.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 0 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076408
X-RAY DIFFRACTIONf_angle_d1.1638726
X-RAY DIFFRACTIONf_dihedral_angle_d22.3887
X-RAY DIFFRACTIONf_chiral_restr0.063998
X-RAY DIFFRACTIONf_plane_restr0.0091134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.38761400.38992838X-RAY DIFFRACTION100
2.32-2.350.41491420.37392945X-RAY DIFFRACTION100
2.35-2.380.36231390.37252898X-RAY DIFFRACTION99
2.38-2.420.41641430.35012885X-RAY DIFFRACTION100
2.42-2.450.36031400.34092898X-RAY DIFFRACTION100
2.45-2.490.40571360.35362844X-RAY DIFFRACTION99
2.49-2.530.35251410.34512950X-RAY DIFFRACTION100
2.53-2.570.39241380.32972852X-RAY DIFFRACTION100
2.57-2.620.38651370.32922902X-RAY DIFFRACTION100
2.62-2.670.40761410.32312910X-RAY DIFFRACTION100
2.67-2.730.3181410.31722875X-RAY DIFFRACTION100
2.73-2.790.36581430.3232905X-RAY DIFFRACTION99
2.79-2.850.35871450.30992886X-RAY DIFFRACTION100
2.85-2.920.32631380.32562883X-RAY DIFFRACTION100
2.92-30.29291390.30692917X-RAY DIFFRACTION100
3-3.090.32821410.31852889X-RAY DIFFRACTION100
3.09-3.190.3271360.30882890X-RAY DIFFRACTION100
3.19-3.30.32271390.2952880X-RAY DIFFRACTION99
3.3-3.430.28961410.28482862X-RAY DIFFRACTION99
3.44-3.590.31581380.26562875X-RAY DIFFRACTION99
3.59-3.780.31391430.25462884X-RAY DIFFRACTION100
3.78-4.020.25031420.22082879X-RAY DIFFRACTION99
4.02-4.330.26281460.20972876X-RAY DIFFRACTION99
4.33-4.760.17631350.1932866X-RAY DIFFRACTION98
4.76-5.450.22161420.19942879X-RAY DIFFRACTION99
5.45-6.860.27131370.22882864X-RAY DIFFRACTION99
6.87-52.50.22931350.19152802X-RAY DIFFRACTION96

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