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- PDB-8jpt: Crystal Structure of the acyltransferase domain from the eighth m... -

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Basic information

Entry
Database: PDB / ID: 8jpt
TitleCrystal Structure of the acyltransferase domain from the eighth module of the spinosad polyketide synthase
ComponentsPolyene macrolide polyketide synthase
KeywordsTRANSFERASE / acyltransferase domain
Function / homology
Function and homology information


toxin biosynthetic process / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / CurL-like, PKS C-terminal / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase dehydratase N-terminal domain / Thioesterase ...Polyketide synthase, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / CurL-like, PKS C-terminal / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase dehydratase N-terminal domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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
Polyene macrolide polyketide synthase
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsHuang, S. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040 China
CitationJournal: Febs J. / Year: 2024
Title: Structural and computational insights into the substrate specificity of acyltransferase domains from modular polyketide synthases.
Authors: Huang, S. / Ji, H. / Zheng, J.
History
DepositionJun 12, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Polyene macrolide polyketide synthase
B: Polyene macrolide polyketide synthase
C: Polyene macrolide polyketide synthase


Theoretical massNumber of molelcules
Total (without water)132,3443
Polymers132,3443
Non-polymers00
Water23413
1
A: Polyene macrolide polyketide synthase


Theoretical massNumber of molelcules
Total (without water)44,1151
Polymers44,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyene macrolide polyketide synthase


Theoretical massNumber of molelcules
Total (without water)44,1151
Polymers44,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyene macrolide polyketide synthase


Theoretical massNumber of molelcules
Total (without water)44,1151
Polymers44,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.345, 154.723, 65.209
Angle α, β, γ (deg.)90.00, 92.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polyene macrolide polyketide synthase / Polyketide synthase extender modules 8-10


Mass: 44114.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnE, A8926_6425 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ALM2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M citric acid pH 5.0, 0.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 29154 / % possible obs: 96.4 % / Redundancy: 3.1 % / CC1/2: 0.947 / CC star: 0.986 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.08 / Rrim(I) all: 0.149 / Χ2: 0.685 / Net I/σ(I): 4.8 / Num. measured all: 90970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.25-3.313.10.43514700.8110.9460.2790.5190.66497.7
3.31-3.373.10.40214440.7730.9340.2580.4790.71697.9
3.37-3.433.10.34114930.8450.9570.220.4070.6997.7
3.43-3.530.28414520.8350.9540.1830.340.73297.4
3.5-3.5830.28614500.8570.9610.1860.3420.88596.4
3.58-3.662.90.24513620.8660.9630.1610.2940.8588.5
3.66-3.753.10.21214340.8880.970.1370.2530.84595.6
3.75-3.853.20.19114990.9060.9750.120.2260.79798.6
3.85-3.973.30.16914480.9250.980.1070.20.83698.5
3.97-4.093.20.14714950.9240.980.0940.1750.77698.2
4.09-4.243.20.14414680.9240.980.0920.1720.7798.4
4.24-4.413.20.12314920.9480.9870.0780.1460.78898.2
4.41-4.613.20.11415080.9430.9850.0730.1360.73898.5
4.61-4.853.10.10314530.9630.990.0650.1220.6797.5
4.85-5.1630.09714750.9670.9910.0610.1150.59397.2
5.16-5.562.90.08513460.9610.990.0550.1020.46488.8
5.56-6.113.30.0914940.9620.990.0570.1070.45798.7
6.11-73.20.07814990.9630.990.0490.0920.42697.9
7-8.813.10.07314650.9780.9950.0460.0860.47396.3
8.81-503.10.07614070.9620.990.0490.0910.52590.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000v718data scaling
HKL-2000v718data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.858 / SU B: 50.775 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25752 1385 4.9 %RANDOM
Rwork0.19786 ---
obs0.20079 26991 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.279 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å2-0 Å20.7 Å2
2---2.43 Å2-0 Å2
3---4.64 Å2
Refinement stepCycle: 1 / Resolution: 3.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9299 0 0 13 9312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129476
X-RAY DIFFRACTIONr_bond_other_d00.0169010
X-RAY DIFFRACTIONr_angle_refined_deg1.091.64112910
X-RAY DIFFRACTIONr_angle_other_deg0.3451.56720635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88751250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.903587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.725101440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.21479
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211651
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022187
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.2944.4225009
X-RAY DIFFRACTIONr_mcbond_other7.2784.4225009
X-RAY DIFFRACTIONr_mcangle_it10.8997.9476256
X-RAY DIFFRACTIONr_mcangle_other10.8997.9486257
X-RAY DIFFRACTIONr_scbond_it9.8345.1054467
X-RAY DIFFRACTIONr_scbond_other9.8335.1054468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.599.0356655
X-RAY DIFFRACTIONr_long_range_B_refined20.16355.4341808
X-RAY DIFFRACTIONr_long_range_B_other20.16455.4341807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.26→3.344 Å
RfactorNum. reflection% reflection
Rfree0.353 87 -
Rwork0.268 1638 -
obs--78.12 %
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)
10.8039-0.5166-0.49890.5530.38680.90950.01520.08290.1634-0.0259-0.02820.0543-0.07160.03230.0130.27550.09780.01130.33720.00310.1678-31.6505-44.601615.5712
20.72540.08690.66910.04450.17391.25890.04160.02470.01510.07220.00150.02610.10920.1367-0.0430.4008-0.1069-0.00820.33290.02330.0974-25.1686-76.928436.8987
30.48880.26330.00211.3109-1.10341.2795-0.06130.0814-0.02490.04990.0932-0.06040.0742-0.3682-0.03180.2971-0.1723-0.05860.57570.04970.0321-56.782-79.1-6.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 441
2X-RAY DIFFRACTION2B24 - 441
3X-RAY DIFFRACTION3C24 - 440

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