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- PDB-8odw: Crystal structure of LbmA Ox-ACP didomain in complex with NADP an... -

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Basic information

Entry
Database: PDB / ID: 8odw
TitleCrystal structure of LbmA Ox-ACP didomain in complex with NADP and ethyl glycinate from the lobatamide PKS (Gynuella sunshinyii)
ComponentsPolyketide synthase modules-related protein
KeywordsBIOSYNTHETIC PROTEIN / Oxime / Polyketide / Oxidase / Biosynthesis
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / Methyltransferase domain 25 / Methyltransferase domain / PKS_PP_betabranch / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain ...Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / Methyltransferase domain 25 / Methyltransferase domain / PKS_PP_betabranch / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ethyl glycinate / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXYGEN MOLECULE / PHOSPHATE ION / Polyketide synthase modules-related protein
Similarity search - Component
Biological speciesGynuella sunshinyii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsFrancois, R.M.M. / Fraley, A.E. / Piel, J. / Weissman, K.J. / Gruez, A.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE93-0002-01 France
European Research Council (ERC)742739European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Modular Oxime Formation by a trans-AT Polyketide Synthase.
Authors: Minas, H.A. / Francois, R.M.M. / Hemmerling, F. / Fraley, A.E. / Dieterich, C.L. / Rudisser, S.H. / Meoded, R.A. / Collin, S. / Weissman, K.J. / Gruez, A. / Piel, J.
History
DepositionMar 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase modules-related protein
B: Polyketide synthase modules-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,60713
Polymers143,9422
Non-polymers3,66511
Water2,360131
1
A: Polyketide synthase modules-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,10710
Polymers71,9711
Non-polymers2,1369
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase modules-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5003
Polymers71,9711
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.751, 206.751, 178.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyketide synthase modules-related protein


Mass: 71971.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gynuella sunshinyii (bacteria) / Gene: YC6258_03642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C5VQJ2

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Non-polymers , 7 types, 142 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GEE / ethyl glycinate


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.8 M Potassium phosphate dibasic/Sodium phosphate monobasic pH 6.0, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980104506016 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980104506016 Å / Relative weight: 1
ReflectionResolution: 3.07→47.84 Å / Num. obs: 42439 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.069 / Rrim(I) all: 0.168 / Χ2: 1 / Net I/σ(I): 9.7
Reflection shellResolution: 3.07→3.18 Å / % possible obs: 96.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.749 / Num. measured all: 24078 / Num. unique obs: 4264 / CC1/2: 0.718 / Rpim(I) all: 0.341 / Rrim(I) all: 0.826 / Χ2: 1.01 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.8data scaling
MOLREP11.9.02phasing
XDSJan 10, 2022data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→44.76 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 2010 4.74 %
Rwork0.2374 --
obs0.24 42381 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9409 0 237 132 9778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.343
X-RAY DIFFRACTIONf_dihedral_angle_d14.9783548
X-RAY DIFFRACTIONf_chiral_restr0.071444
X-RAY DIFFRACTIONf_plane_restr0.0091717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.140.37141360.27982709X-RAY DIFFRACTION95
3.14-3.230.31291470.26582830X-RAY DIFFRACTION100
3.23-3.320.31841450.232832X-RAY DIFFRACTION100
3.32-3.430.25581390.22062855X-RAY DIFFRACTION100
3.43-3.550.28361570.21782854X-RAY DIFFRACTION100
3.55-3.690.25471500.20272859X-RAY DIFFRACTION100
3.69-3.860.28251330.19412866X-RAY DIFFRACTION100
3.86-4.070.22151330.18782882X-RAY DIFFRACTION100
4.07-4.320.2411420.17752888X-RAY DIFFRACTION100
4.32-4.650.22371520.1782875X-RAY DIFFRACTION100
4.65-5.120.23521500.19212902X-RAY DIFFRACTION100
5.12-5.860.30591330.24522944X-RAY DIFFRACTION100
5.86-7.380.35231360.30173003X-RAY DIFFRACTION100
7.38-44.760.40981570.34893072X-RAY DIFFRACTION98

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