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- PDB-8ia9: SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in ... -

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Basic information

Entry
Database: PDB / ID: 8ia9
TitleSpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with Mg
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 / Demethylmacrocin O-methyltransferase
Function and homology information
Biological speciesSaccharopolyspora spinosa (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: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,0744
Polymers87,0252
Non-polymers492
Water2,792155
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)174,1488
Polymers174,0514
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area19930 Å2
ΔGint-101 kcal/mol
Surface area55280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.114, 134.114, 159.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-573-

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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.09 Å3/Da / Density % sol: 69.94 %
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 28, 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: 51119 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.129 / Χ2: 0.038 / Net I/σ(I): 5.1 / Num. measured all: 645766
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.5412.80.79625051.0021100
2.54-2.5912.70.69825090.9921100
2.59-2.6412.60.6525140.9941100
2.64-2.6912.50.53425211.0051100
2.69-2.7511.90.46225071.011100
2.75-2.8211.10.39925271.033199.9
2.82-2.89130.37525161.0251100
2.89-2.9613.20.33125271.0141100
2.96-3.0513.10.29125181.0371100
3.05-3.1513.10.22825351.0471100
3.15-3.2612.90.19425491.0441100
3.26-3.3912.90.16425181.041100
3.39-3.5512.40.13225541.0281100
3.55-3.7311.50.10925481.0051100
3.73-3.9713.60.10325600.9971100
3.97-4.2713.50.09125660.971100
4.27-4.713.20.08525880.9561100
4.7-5.38120.08326120.909199.9
5.38-6.7813.10.08826350.9651100
6.78-5011.60.08128101.05199.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000v718-Linuxdata reduction
HKL-2000v718-Linuxdata scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.46 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.72 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24327 2606 5.2 %RANDOM
Rwork0.20783 ---
obs0.20964 47477 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5869 0 2 155 6026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136006
X-RAY DIFFRACTIONr_bond_other_d00.0175636
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.6418167
X-RAY DIFFRACTIONr_angle_other_deg1.1751.57412967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33221.03330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3611552
X-RAY DIFFRACTIONr_chiral_restr0.0540.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.026889
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021389
X-RAY DIFFRACTIONr_mcbond_it3.9592.7613024
X-RAY DIFFRACTIONr_mcbond_other3.9032.7583023
X-RAY DIFFRACTIONr_mcangle_it6.2294.1183773
X-RAY DIFFRACTIONr_mcangle_other6.2384.1223774
X-RAY DIFFRACTIONr_scbond_it4.2913.0232982
X-RAY DIFFRACTIONr_scbond_other4.2913.0262983
X-RAY DIFFRACTIONr_scangle_other7.0054.4284395
X-RAY DIFFRACTIONr_long_range_B_refined10.65649.87724163
X-RAY DIFFRACTIONr_long_range_B_other10.65949.86824112
Refine LS restraints NCS

Ens-ID: 1 / Number: 11351 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.562 Å
RfactorNum. reflection% reflection
Rfree0.318 154 -
Rwork0.245 2967 -
obs--84.06 %
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)
10.52910.35450.05540.59620.12130.0344-0.15290.21150.05570.0110.12920.24690.02510.03560.02370.0989-0.03580.00610.1101-0.02490.2017-49.5469-36.254-12.0697
20.5210.24950.01320.4743-0.0590.0194-0.10840.1922-0.08080.02090.1002-0.2057-0.0329-0.00680.00820.0832-0.02130.02140.1039-0.00070.1509-17.7485-31.7845-11.6417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 387
2X-RAY DIFFRACTION2B3 - 388

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