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- PDB-8iaa: SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in ... -

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Basic information

Entry
Database: PDB / ID: 8iaa
TitleSpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with SAH
ComponentsDemethylmacrocin O-methyltransferase
KeywordsTRANSFERASE / Methyltransferase
Function / homologyMethyltransferase MycE, N-terminal / MycE methyltransferase N-terminal / antibiotic biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / metal ion binding / S-ADENOSYL-L-HOMOCYSTEINE / Demethylmacrocin O-methyltransferase
Function and homology information
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHuang, S. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn.
Authors: Huang, S. / Ji, H. / Zheng, J.
History
DepositionFeb 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Demethylmacrocin O-methyltransferase
B: Demethylmacrocin O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8436
Polymers87,0252
Non-polymers8174
Water6,449358
1
A: Demethylmacrocin O-methyltransferase
B: Demethylmacrocin O-methyltransferase
hetero molecules

A: Demethylmacrocin O-methyltransferase
B: Demethylmacrocin O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,68612
Polymers174,0514
Non-polymers1,6358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area19720 Å2
ΔGint-125 kcal/mol
Surface area54510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.975, 133.975, 160.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

21B-665-

HOH

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Components

#1: Protein Demethylmacrocin O-methyltransferase


Mass: 43512.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ALN2
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM Sodium citrate, pH 6.3, 34% v/v PEG 200, 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 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 85935 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.029 / Rrim(I) all: 0.101 / Χ2: 0.998 / Net I/σ(I): 5.7 / Num. measured all: 988878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1411.90.89842410.8570.9610.2680.9380.933100
2.14-2.1811.90.78642060.8760.9660.2350.8210.953100
2.18-2.2211.70.73742300.8910.9710.2220.7710.96100
2.22-2.2611.70.63142570.9040.9740.190.6590.967100
2.26-2.3111.60.53842240.9370.9830.1630.5630.983100
2.31-2.3711.40.44242770.9480.9870.1350.4621.006100
2.37-2.4211.10.36442090.9630.9910.1130.3811.01100
2.42-2.4910.20.33642630.9640.9910.110.3541.018100
2.49-2.5611.80.28242650.9810.9950.0850.2941.029100
2.56-2.65120.24342700.9820.9960.0730.2541.032100
2.65-2.7411.90.19742600.9890.9970.0590.2051.058100
2.74-2.8511.80.16242620.9920.9980.0490.171.057100
2.85-2.9811.70.14242890.9940.9980.0430.1481.07100
2.98-3.1411.30.11542880.9950.9990.0360.121.089100
3.14-3.3310.80.08743030.9960.9990.0280.0921.10599.9
3.33-3.5912.20.07243130.9980.9990.0220.0761.077100
3.59-3.95120.06143550.99810.0180.0641.037100
3.95-4.5211.40.05243620.99910.0160.0540.969100
4.52-5.711.20.04744110.99910.0140.0490.841100
5.7-5010.70.04446500.99910.0140.0460.76299.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000v718data scaling
HKL-2000v718data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.63 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.724 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22781 4225 5 %RANDOM
Rwork0.20131 ---
obs0.20263 80023 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5924 0 54 358 6336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0136132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155714
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.6438344
X-RAY DIFFRACTIONr_angle_other_deg1.4991.57513148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1665764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28221.131336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99515954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0331552
X-RAY DIFFRACTIONr_chiral_restr0.0930.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021424
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_it2.1482.1393068
X-RAY DIFFRACTIONr_mcbond_other2.1482.1393068
X-RAY DIFFRACTIONr_mcangle_it3.5123.1933828
X-RAY DIFFRACTIONr_mcangle_other3.5113.1933829
X-RAY DIFFRACTIONr_scbond_it2.3332.3353064
X-RAY DIFFRACTIONr_scbond_other2.3332.3353064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.753.4344517
X-RAY DIFFRACTIONr_long_range_B_refined7.06439.44125664
X-RAY DIFFRACTIONr_long_range_B_other7.04339.36125532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 247 -
Rwork0.254 5232 -
obs--87.99 %
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)
10.3732-0.20720.08640.42790.0120.03760.07170.00420.1328-0.158-0.0857-0.0724-0.0026-0.02580.01410.07460.0160.02140.04860.02720.087931.8521-17.463627.9399
20.4871-0.2582-0.120.4520.06450.03930.09770.0178-0.1806-0.1576-0.11560.0398-0.0350.00930.01790.06580.02280.00240.0542-0.02010.128136.1803-49.643327.4594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 401
2X-RAY DIFFRACTION2B4 - 401

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