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- PDB-8r2r: N-terminal domain of the Mycobacterium tuberculosis fatty acyl Co... -

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Basic information

Entry
Database: PDB / ID: 8r2r
TitleN-terminal domain of the Mycobacterium tuberculosis fatty acyl CoA synthetase, FadD5
ComponentsProbable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
KeywordsLIGASE / FadD5 / Fatty acyl CoA synthetase / Mycobacterium tuberculosis / mce1 operon
Function / homology
Function and homology information


acid-thiol ligase activity / CoA-ligase activity
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
Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsRahman, M.A. / Dalwani, S. / Venkatesan, R.
Funding supportEuropean Union, Finland, 6items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission713606European Union
Academy of Finland332967 Finland
Other privateSigrid Juselius Foundation
Other privateTampere Tuberculosis Foundation
Other governmentUniversity of Oulu
Jane and Aatos Erkko Foundation Finland
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis.
Authors: Rahman, M.A. / Dalwani, S. / Venkatesan, R.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
B: Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9626
Polymers101,5942
Non-polymers3684
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-20 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.671, 121.671, 249.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)


Mass: 50796.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Construct of N-terminal domain alone (1-456)
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadD5, Rv0166 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07411
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.75 Å3/Da / Density % sol: 74.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium formate, 20 % w/v SOKALAN CP 45

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.47→62.47 Å / Num. obs: 67795 / % possible obs: 99.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 73.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 1.9 % / Num. unique obs: 4491 / CC1/2: 0.339 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→60.84 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 3325 4.99 %
Rwork0.1979 63279 -
obs0.1991 66604 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.79 Å2
Refinement stepCycle: LAST / Resolution: 2.47→60.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 24 35 6255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386341
X-RAY DIFFRACTIONf_angle_d0.62588644
X-RAY DIFFRACTIONf_chiral_restr0.04521011
X-RAY DIFFRACTIONf_plane_restr0.0071123
X-RAY DIFFRACTIONf_dihedral_angle_d12.43362280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.510.3927980.38511782X-RAY DIFFRACTION67.7
2.51-2.540.36791340.35422532X-RAY DIFFRACTION95.18
2.54-2.580.34321370.34282590X-RAY DIFFRACTION97.99
2.58-2.620.35361250.31942619X-RAY DIFFRACTION98.81
2.62-2.670.28211440.31332625X-RAY DIFFRACTION99.14
2.67-2.720.31761540.30162623X-RAY DIFFRACTION99
2.72-2.770.32191180.30422653X-RAY DIFFRACTION99.18
2.77-2.830.36761270.31442652X-RAY DIFFRACTION99.43
2.83-2.890.37371340.33322644X-RAY DIFFRACTION99.32
2.89-2.960.30251360.28882652X-RAY DIFFRACTION99.32
2.96-3.030.27211420.25422643X-RAY DIFFRACTION99.29
3.03-3.110.30131310.23052654X-RAY DIFFRACTION99.46
3.11-3.20.27491310.22252684X-RAY DIFFRACTION99.29
3.2-3.310.2311370.22392653X-RAY DIFFRACTION99.64
3.31-3.430.26051350.22432653X-RAY DIFFRACTION99.46
3.43-3.560.28451560.24062681X-RAY DIFFRACTION99.72
3.56-3.720.22431430.2012675X-RAY DIFFRACTION99.72
3.72-3.920.21071370.1732718X-RAY DIFFRACTION99.65
3.92-4.170.20531570.1522660X-RAY DIFFRACTION99.79
4.17-4.490.18841630.15082703X-RAY DIFFRACTION99.86
4.49-4.940.17131410.14322732X-RAY DIFFRACTION100
4.94-5.650.1841590.1632740X-RAY DIFFRACTION99.9
5.65-7.120.22091310.19022818X-RAY DIFFRACTION99.93
7.12-60.840.16291550.17152893X-RAY DIFFRACTION97.97
Refinement TLS params.Method: refined / Origin x: -24.5617048048 Å / Origin y: 50.3279204695 Å / Origin z: 25.6018109724 Å
111213212223313233
T0.431956799038 Å2-0.00674160095405 Å20.00206318840561 Å2-0.364577172153 Å20.0246399298353 Å2--0.428513890612 Å2
L0.866989400042 °20.00114605147869 °20.093998865632 °2-0.942699706025 °2-0.516580652014 °2--1.62338779739 °2
S-0.00855042788867 Å °-0.0269737345333 Å °0.031342983881 Å °0.0750545538216 Å °0.0690054747928 Å °-0.0303887065563 Å °0.0898463954977 Å °-0.0309389446558 Å °-0.0677406315722 Å °
Refinement TLS groupSelection details: all

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