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- PDB-9fce: BelI in complex with SAM from Streptomyces sp. UCK14 -

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Basic information

Entry
Database: PDB / ID: 9fce
TitleBelI in complex with SAM from Streptomyces sp. UCK14
ComponentsSAM dependent methyltransferase
KeywordsTRANSFERASE / Natural Product Biosynthesis / Enzyme Mechanism / Metal Ion interaction / Molecular Docking / Structure Function Relationships
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / (R,R)-2,3-BUTANEDIOL / S-ADENOSYLMETHIONINE / SAM dependent methyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Deciphering the SAM- and metal-dependent mechanism of O-methyltransferases in cystargolide and belactosin biosynthesis: A structure-activity relationship study.
Authors: Kuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM dependent methyltransferase
B: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7528
Polymers50,7232
Non-polymers1,0296
Water2,702150
1
A: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9525
Polymers25,3621
Non-polymers5914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8003
Polymers25,3621
Non-polymers4392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.430, 165.000, 165.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SAM dependent methyltransferase


Mass: 25361.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: belI / Plasmid: pETDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6R583

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Non-polymers , 5 types, 156 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M LiCl, 0.1 M TRIS, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 38727 / % possible obs: 95.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.9
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 21464 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 8.266 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20748 1936 5 %RANDOM
Rwork0.17031 ---
obs0.17234 36781 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.256 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å20 Å2
2--2.68 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 66 152 3486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163243
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.8364627
X-RAY DIFFRACTIONr_angle_other_deg0.421.7547419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.824538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28410534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
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_it7.5214.7491670
X-RAY DIFFRACTIONr_mcbond_other7.5174.7491670
X-RAY DIFFRACTIONr_mcangle_it11.3188.5312077
X-RAY DIFFRACTIONr_mcangle_other11.3168.5312078
X-RAY DIFFRACTIONr_scbond_it7.775.0911734
X-RAY DIFFRACTIONr_scbond_other7.7695.0911734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.949.2212551
X-RAY DIFFRACTIONr_long_range_B_refined17.543.563781
X-RAY DIFFRACTIONr_long_range_B_other17.27143.453758
X-RAY DIFFRACTIONr_rigid_bond_restr2.40436647
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 145 -
Rwork0.379 2755 -
obs--97.51 %
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)
10.4705-0.258-0.3440.2319-0.03420.8047-0.00570.0228-0.0481-0.01890.01530.04550.0445-0.087-0.00970.0479-0.0075-0.00840.01020.00230.03-25.018923.9866-17.729
20.04220.0478-0.00110.1174-0.05210.0430.00030.0022-0.0027-0.0043-0.0062-0.01070.00580.00780.0060.04680.0025-0.00020.00170.00140.01784.3623.5301-16.9855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 803
2X-RAY DIFFRACTION2B15 - 801

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