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- PDB-8iqu: Structure of MtbFadD23 with PhU-AMS -

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Basic information

Entry
Database: PDB / ID: 8iqu
TitleStructure of MtbFadD23 with PhU-AMS
ComponentsFatty-acid-CoA ligase FadD23
KeywordsLIGASE / long-chain-fatty-acid-AMP ligase
Function / homology
Function and homology information


long-chain-fatty-acid-CoA ligase / long-chain fatty acid-CoA ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / lipid biosynthetic process / membrane
Similarity search - Function
Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine / Fatty-acid-AMP ligase FadD23 (Fatty-acid-AMP synthetase) (Fatty-acid-AMP synthase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsYan, M.R. / Zhang, W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100142 China
National Natural Science Foundation of China (NSFC)32171259 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structural basis for the development of potential inhibitors targeting FadD23 from Mycobacterium tuberculosis.
Authors: Yan, M. / Ma, M. / Chen, R. / Cao, Y. / Zhang, W. / Liu, X.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty-acid-CoA ligase FadD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8092
Polymers65,2021
Non-polymers6071
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.921, 72.921, 457.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Fatty-acid-CoA ligase FadD23


Mass: 65202.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: fadD_1, fadD, fadD_2, ERS007657_01090, ERS007661_00211, ERS007663_00248, ERS007665_00157, ERS007670_01303, ERS007679_02742, ERS007681_00438, ERS007703_00976, ERS007720_00031, ERS007722_00970, ...Gene: fadD_1, fadD, fadD_2, ERS007657_01090, ERS007661_00211, ERS007663_00248, ERS007665_00157, ERS007670_01303, ERS007679_02742, ERS007681_00438, ERS007703_00976, ERS007720_00031, ERS007722_00970, ERS027646_00328, ERS027661_00390, SAMEA2683035_00029
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E8J579, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases, long-chain-fatty-acid-CoA ligase
#2: Chemical ChemComp-649 / 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine


Mass: 606.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 30 mM Tris (pH 8.5), 140 mM sodium citrate, 60 mM ammonium phosphate monobasic, 15% w/v (+/-)-2-methyl-2,4-pentanediol, and 14% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 22577 / % possible obs: 99.97 % / Redundancy: 10.3 % / CC1/2: 0.997 / Net I/σ(I): 9.21
Reflection shellResolution: 2.64→2.8 Å / Num. unique obs: 1613 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3600refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.65 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1174 5.2 %
Rwork0.2032 --
obs0.2053 22577 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 42 69 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064289
X-RAY DIFFRACTIONf_angle_d0.9815850
X-RAY DIFFRACTIONf_dihedral_angle_d9.901602
X-RAY DIFFRACTIONf_chiral_restr0.062678
X-RAY DIFFRACTIONf_plane_restr0.009757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.760.34171330.30492586X-RAY DIFFRACTION100
2.76-2.910.34131750.26182561X-RAY DIFFRACTION100
2.91-3.090.30081360.25692605X-RAY DIFFRACTION100
3.09-3.330.27561420.25182654X-RAY DIFFRACTION100
3.33-3.660.28551480.21612615X-RAY DIFFRACTION100
3.66-4.190.24831340.18412677X-RAY DIFFRACTION100
4.19-5.280.21121510.16492743X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2021-0.08510.0083.03020.47292.59870.04450.2486-0.4127-0.30190.0348-0.12370.22770.0068-0.07890.3054-0.03180.00670.5373-0.09350.42835.6444-42.6926-11.8143
21.4734-0.2017-0.85922.74950.08861.7982-0.1059-0.2160.1837-0.23110.10410.11-0.2556-0.24430.00990.337-0.0122-0.06580.6366-0.05950.4117-3.8459-20.0093-11.6736
33.65891.3546-0.21945.36420.27964.9337-0.55320.1227-0.55970.6522-0.1980.46271.0583-0.39370.75810.73040.0010.25210.4697-0.11290.67520.9995-12.4187-33.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 243 )
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 460 )
3X-RAY DIFFRACTION3chain 'A' and (resid 461 through 576 )

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