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- PDB-6neg: N191D, F205S mutant of scoulerine-9-O methyltransferase from Thal... -

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Basic information

Entry
Database: PDB / ID: 6neg
TitleN191D, F205S mutant of scoulerine-9-O methyltransferase from Thalictrum flavum complexed with S-ADENOSYL-L-HOMOCYSTEINE
Components(S)-scoulerine 9-O-methyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Scoulerine / Methyltransferase / Benzylisoquinoline Alkaloid / Plant natural products
Function / homology
Function and homology information


(S)-scoulerine 9-O-methyltransferase / (S)-scoulerine 9-O-methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / (S)-scoulerine 9-O-methyltransferase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsValentic, T.R. / Smolke, C.D. / Payne, J.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DP1AT007886-05 United States
CitationJournal: To Be Published
Title: Structural and functional characterization of the scoulerine 9-O methyltransferase from Thalictrum flavum.
Authors: Valentic, T.R. / Smolke, C.S. / Payne, J.T.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-scoulerine 9-O-methyltransferase
B: (S)-scoulerine 9-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2484
Polymers81,4792
Non-polymers7692
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-71 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.600, 84.240, 67.480
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein (S)-scoulerine 9-O-methyltransferase


Mass: 40739.621 Da / Num. of mol.: 2 / Mutation: N191D, F205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5C9L2, (S)-scoulerine 9-O-methyltransferase
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 273.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3,350 and 0.22 M AMSO4

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Data collection

DiffractionMean temperature: 104.3 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.180763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.180763 Å / Relative weight: 1
ReflectionResolution: 1.95→84.24 Å / Num. obs: 51180 / % possible obs: 96.3 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 15.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3604 / CC1/2: 0.907 / Rpim(I) all: 0.328 / Rrim(I) all: 0.622 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3reo

3reo


Resolution: 1.95→52.476 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 2000 3.91 %
Rwork0.1739 --
obs0.1749 51149 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→52.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 52 404 5736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095448
X-RAY DIFFRACTIONf_angle_d0.8967390
X-RAY DIFFRACTIONf_dihedral_angle_d19.3631982
X-RAY DIFFRACTIONf_chiral_restr0.079846
X-RAY DIFFRACTIONf_plane_restr0.005948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.26061390.24043517X-RAY DIFFRACTION96
1.9988-2.05280.26491460.21723487X-RAY DIFFRACTION96
2.0528-2.11320.23341460.20223502X-RAY DIFFRACTION96
2.1132-2.18140.19041410.1833492X-RAY DIFFRACTION97
2.1814-2.25940.22141450.18833511X-RAY DIFFRACTION96
2.2594-2.34990.22391320.18093275X-RAY DIFFRACTION90
2.3499-2.45680.19791310.17753329X-RAY DIFFRACTION92
2.4568-2.58630.21621470.17393571X-RAY DIFFRACTION98
2.5863-2.74840.20261420.17473615X-RAY DIFFRACTION98
2.7484-2.96060.20731460.18223607X-RAY DIFFRACTION98
2.9606-3.25840.19791510.18133607X-RAY DIFFRACTION98
3.2584-3.72980.19361470.16843591X-RAY DIFFRACTION98
3.7298-4.69870.18331320.14833339X-RAY DIFFRACTION90
4.6987-52.4950.1811550.16713706X-RAY DIFFRACTION99
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)
11.10280.02860.27470.35040.24311.54220.07130.0606-0.0696-0.0096-0.0640.03120.0419-0.1998-0.01490.25370.017-0.00370.21830.01460.2414.47282.698413.7309
20.91070.05310.60670.04150.11380.4424-0.31670.14310.91110.17270.01270.1153-0.46560.3441-0.03050.40690.05160.00290.37240.0620.457413.525522.128334.9982
31.58340.2005-0.12431.37750.02541.87570.03430.0436-0.05160.0620.08070.0875-0.0551-0.2188-0.06660.19770.03030.00210.24380.03150.23882.56523.970242.3596
41.3710.36290.30840.33610.07291.63390.0553-0.1744-0.09660.0364-0.1038-0.061-0.06140.12460.0010.22260.015-0.00190.20530.0160.243829.92546.929329.3327
52.08631.48340.98611.0320.69150.4644-0.1752-0.53280.7969-0.0477-0.23470.4258-0.1337-0.47570.02040.42420.05130.03190.3647-0.04380.392121.950323.68326.9695
61.45190.5074-0.13261.4677-0.3351.99140.0391-0.07880.02810.0213-0.0746-0.2701-0.22060.328-0.00910.2589-0.03970.01570.25320.00120.253546.129817.45134.5197
71.46550.2387-0.10061.1574-0.45811.9740.02290.0704-0.1297-0.14060.0075-0.02320.09440.01840.02810.26010.0229-0.0040.2226-0.01350.223435.26177.7463-2.6973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 351 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 132 )
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 154 )
6X-RAY DIFFRACTION6chain 'B' and (resid 155 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 350 )

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