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- PDB-8jpu: Crystal Structure of the acyltransferase domain from the fifth mo... -

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Basic information

Entry
Database: PDB / ID: 8jpu
TitleCrystal Structure of the acyltransferase domain from the fifth module of the tylosin polyketide synthase
ComponentsTylactone synthase modules 4 & 5
KeywordsTRANSFERASE / acyltransferase
Function / homology
Function and homology information


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 / oxidoreductase activity / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / CurL-like, PKS C-terminal / 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, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / CurL-like, PKS C-terminal / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / 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, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Tylactone synthase modules 4 & 5
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, S. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040 China
CitationJournal: To Be Published
Title: Structural Insights into the Substrate Specificity of Acyltransferases from Tylosin Polyketide Synthase and Spinosad Polyketide Synthase
Authors: Huang, S. / Zheng, J.
History
DepositionJun 12, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tylactone synthase modules 4 & 5
B: Tylactone synthase modules 4 & 5
C: Tylactone synthase modules 4 & 5
D: Tylactone synthase modules 4 & 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,6918
Polymers186,3074
Non-polymers3844
Water52229
1
A: Tylactone synthase modules 4 & 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6732
Polymers46,5771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-21 kcal/mol
Surface area16950 Å2
MethodPISA
2
B: Tylactone synthase modules 4 & 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6732
Polymers46,5771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-22 kcal/mol
Surface area15510 Å2
MethodPISA
3
C: Tylactone synthase modules 4 & 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6732
Polymers46,5771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-21 kcal/mol
Surface area16950 Å2
MethodPISA
4
D: Tylactone synthase modules 4 & 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6732
Polymers46,5771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-21 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.949, 138.376, 209.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tylactone synthase modules 4 & 5


Mass: 46576.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O33956
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 7.5, 29% PEG3350,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: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 52874 / % possible obs: 78.2 % / Redundancy: 6.1 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.043 / Rrim(I) all: 0.118 / Χ2: 0.862 / Net I/σ(I): 5.5 / Num. measured all: 324871
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.50.74524760.7270.9180.3130.8170.91174.2
2.54-2.595.50.62325740.7780.9360.2620.6820.90477.8
2.59-2.645.40.56625380.8140.9480.2390.6210.89275.5
2.64-2.695.50.49325440.8540.960.210.5420.90977
2.69-2.755.20.45424960.870.9650.1960.50.90674.7
2.75-2.825.20.3724830.8980.9730.1620.4090.94474.1
2.82-2.895.40.34126750.9130.9770.1430.3730.88180.1
2.89-2.965.70.29627320.940.9840.1220.3230.88882.4
2.96-3.055.70.25527260.9430.9850.1050.2780.86781.2
3.05-3.155.70.21627510.9720.9930.090.2360.87181.6
3.15-3.265.90.17127950.9810.9950.070.1860.87383.6
3.26-3.3960.1427270.9830.9960.0570.1530.85881.4
3.39-3.5560.10727000.9890.9970.0430.1160.90279.8
3.55-3.736.10.08225420.9930.9980.0320.0890.8375.8
3.73-3.976.70.07127600.9950.9990.0270.0760.84481.8
3.97-4.276.90.05927520.9970.9990.0220.0630.81780.7
4.27-4.770.05127120.9970.9990.0180.0540.81279.4
4.7-5.387.20.05125770.9980.9990.0180.0550.78875.2
5.38-6.788.10.05826860.9940.9980.0190.0610.79377.2
6.78-507.80.04226280.9980.9990.0140.0440.8671.6

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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: 2.5→39.46 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 24.54 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26301 2453 4.9 %RANDOM
Rwork0.20228 ---
obs0.20526 47448 73.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å20 Å2
2---1.3 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.5→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11950 0 20 29 11999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212842
X-RAY DIFFRACTIONr_bond_other_d00.01612179
X-RAY DIFFRACTIONr_angle_refined_deg0.8341.64917467
X-RAY DIFFRACTIONr_angle_other_deg0.2911.57727984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57251656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.8215124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31102030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0420.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022866
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_it5.9054.356636
X-RAY DIFFRACTIONr_mcbond_other5.9054.356635
X-RAY DIFFRACTIONr_mcangle_it9.8647.8088288
X-RAY DIFFRACTIONr_mcangle_other9.8647.8098289
X-RAY DIFFRACTIONr_scbond_it5.6054.7376206
X-RAY DIFFRACTIONr_scbond_other5.6044.7396203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5958.5189174
X-RAY DIFFRACTIONr_long_range_B_refined18.74852.1754861
X-RAY DIFFRACTIONr_long_range_B_other18.74852.1754860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å
RfactorNum. reflection% reflection
Rfree0.373 132 -
Rwork0.287 2673 -
obs--56.94 %
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)
10.5353-0.0878-0.01540.4816-0.1090.02750.03610.0391-0.06960.0356-0.02930.0385-0.010.01-0.00680.00820.014-0.00480.09690.00380.10846.168917.252148.291
20.98720.1176-0.0240.1253-0.10010.09280.0143-0.03960.1636-0.0112-0.02550.03490.00940.00760.01120.0025-0.0014-0.00680.0861-0.04020.145539.034446.979351.0894
30.605-0.23770.03150.31170.00070.00260.02110.06310.1170.0329-0.0306-0.02460.003400.00950.00850.00250.00640.07120.03580.15521.468449.2532102.3781
40.86950.0907-0.02550.0527-0.08960.17990.022-0.04070.13080.0073-0.01530.0179-0.01410.0096-0.00670.0059-0.0018-0.00660.0911-0.02330.129813.4821-19.7319105.0821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 500
2X-RAY DIFFRACTION2B54 - 500
3X-RAY DIFFRACTION3C54 - 500
4X-RAY DIFFRACTION4D54 - 500

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