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- PDB-9cfj: Fluvirucin Thioesterase Domain (FluC TE) -

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Basic information

Entry
Database: PDB / ID: 9cfj
TitleFluvirucin Thioesterase Domain (FluC TE)
ComponentsFluC
KeywordsHYDROLASE / thioesterase domain / natural products / PKS
Function / homology
Function and homology information


toxin biosynthetic process / [acyl-carrier-protein] S-acetyltransferase activity / macrolide biosynthetic process / fatty acyl-[ACP] hydrolase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / DIM/DIP cell wall layer assembly / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding ...toxin biosynthetic process / [acyl-carrier-protein] S-acetyltransferase activity / macrolide biosynthetic process / fatty acyl-[ACP] hydrolase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / DIM/DIP cell wall layer assembly / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain ...Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesActinomadura vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsChoudhary, V. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK042303 United States
CitationJournal: Acs Catalysis / Year: 2024
Title: Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation.
Authors: McCullough, T.M. / Choudhary, V. / Akey, D.L. / Skiba, M.A. / Bernard, S.M. / Kittendorf, J.D. / Schmidt, J.J. / Sherman, D.H. / Smith, J.L.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FluC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9746
Polymers30,2211
Non-polymers7535
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10 kcal/mol
Surface area12220 Å2
Unit cell
Length a, b, c (Å)132.752, 132.752, 48.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-2720-

HOH

21A-2740-

HOH

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Components

#1: Protein FluC


Mass: 30221.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura vulgaris (bacteria) / Gene: fluC / Production host: Escherichia coli (E. coli) / References: UniProt: K4I6L4
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, 30% (v/v) PEG 400, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.44→38.32 Å / Num. obs: 88675 / % possible obs: 99.77 % / Redundancy: 19.7 % / Biso Wilson estimate: 23.61 Å2 / CC1/2: 1 / Net I/σ(I): 26.5
Reflection shellResolution: 1.44→1.53 Å / Num. unique obs: 2751 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→38.32 Å / SU ML: 0.2484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 4339 4.89 %
Rwork0.1561 84336 -
obs0.1574 88675 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.76 Å2
Refinement stepCycle: LAST / Resolution: 1.44→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 42 375 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532495
X-RAY DIFFRACTIONf_angle_d0.74983414
X-RAY DIFFRACTIONf_chiral_restr0.0749348
X-RAY DIFFRACTIONf_plane_restr0.0062473
X-RAY DIFFRACTIONf_dihedral_angle_d14.879966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.59741350.60912616X-RAY DIFFRACTION93.25
1.46-1.470.54951460.50552796X-RAY DIFFRACTION99.93
1.47-1.490.43831530.42752775X-RAY DIFFRACTION100
1.49-1.510.30781630.32552775X-RAY DIFFRACTION100
1.51-1.530.30851610.2852762X-RAY DIFFRACTION100
1.53-1.550.24761430.2372809X-RAY DIFFRACTION100
1.55-1.570.24391630.21112795X-RAY DIFFRACTION99.97
1.57-1.60.25451690.19882752X-RAY DIFFRACTION100
1.6-1.620.2361370.20542846X-RAY DIFFRACTION100
1.62-1.650.25561330.22552784X-RAY DIFFRACTION100
1.65-1.680.28831170.24632814X-RAY DIFFRACTION100
1.68-1.710.18471400.14992795X-RAY DIFFRACTION100
1.71-1.740.23011280.1362858X-RAY DIFFRACTION100
1.74-1.770.17671500.13532787X-RAY DIFFRACTION100
1.77-1.810.16971560.13212802X-RAY DIFFRACTION100
1.81-1.850.16871680.12972787X-RAY DIFFRACTION100
1.85-1.90.16731640.13462772X-RAY DIFFRACTION100
1.9-1.950.15441320.13192837X-RAY DIFFRACTION100
1.95-2.010.16331410.12542835X-RAY DIFFRACTION100
2.01-2.080.1521210.13052808X-RAY DIFFRACTION100
2.08-2.150.18171420.13422803X-RAY DIFFRACTION100
2.15-2.240.16241420.13192848X-RAY DIFFRACTION100
2.24-2.340.17281570.13142795X-RAY DIFFRACTION100
2.34-2.460.17341540.14332826X-RAY DIFFRACTION100
2.46-2.610.19681380.14892826X-RAY DIFFRACTION100
2.61-2.820.1921400.15362849X-RAY DIFFRACTION100
2.82-3.10.18711460.15592841X-RAY DIFFRACTION100
3.1-3.550.16931310.15592873X-RAY DIFFRACTION100
3.55-4.470.15121470.14352881X-RAY DIFFRACTION100
4.47-38.320.17781220.16152989X-RAY DIFFRACTION99.9

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