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- PDB-5icf: Crystal structure of (S)-norcoclaurine 6-O-methyltransferase with... -

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Basic information

Entry
Database: PDB / ID: 5icf
TitleCrystal structure of (S)-norcoclaurine 6-O-methyltransferase with S-adenosyl-L-homocysteine and sanguinarine
Components(S)-norcoclaurine 6-O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / benzylisoquinoline alkaloid
Function / homology
Function and homology information


(RS)-norcoclaurine 6-O-methyltransferase / (RS)-norcoclaurine 6-O-methyltransferase activity / alkaloid metabolic process / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Chem-SAU / (RS)-norcoclaurine 6-O-methyltransferase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRobin, A.Y. / Graindorge, M. / Giustini, C. / Dumas, R. / Matringe, M.
Funding support France, 1items
OrganizationGrant numberCountry
INRA (French National Institute for Agricultural Research)P-BV-2 France
CitationJournal: Plant J. / Year: 2016
Title: Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.
Authors: Robin, A.Y. / Giustini, C. / Graindorge, M. / Matringe, M. / Dumas, R.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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)-norcoclaurine 6-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31321
Polymers39,5321
Non-polymers1,78120
Water4,053225
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint31 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.340, 109.090, 40.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-403-

K

21A-621-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein (S)-norcoclaurine 6-O-methyltransferase


Mass: 39531.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant)
Production host: Escherichia coli (E. coli)
References: UniProt: Q5C9L7, (RS)-norcoclaurine 6-O-methyltransferase

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Non-polymers , 7 types, 245 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SAU / 13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium / Sanguinarine


Mass: 332.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14NO4 / Comment: alkaloid*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Peg3350, Sodium Citrate, Phosphate Citrate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 31050 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 23.147 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.69
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.90.2874.95196.5
1.9-2.10.1698.57199.9
2.1-2.40.09813.97199.8
2.4-2.80.06420.29199.8
2.8-3.80.03531.61199.7
3.8-5.80.02444.131100
5.8-8.80.01940.95199.7
8.80.01643.64194.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.384 / SU ML: 0.075 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1553 5 %RANDOM
Rwork0.1564 ---
obs0.1583 31049 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.13 Å2 / Biso mean: 17.955 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å20 Å2
2---0.89 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.8→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 118 225 3088
Biso mean--26.74 26.61 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193060
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9944166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5545402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63625.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96715539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.603157
X-RAY DIFFRACTIONr_chiral_restr0.1550.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212249
X-RAY DIFFRACTIONr_mcbond_it1.6561.5741469
X-RAY DIFFRACTIONr_mcangle_it2.4272.3561849
X-RAY DIFFRACTIONr_scbond_it2.8291.8231589
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 111 -
Rwork0.203 2109 -
all-2220 -
obs--97.97 %

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