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- PDB-5icg: Crystal structure of apo (S)-norcoclaurine 6-O-methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5icg
TitleCrystal structure of apo (S)-norcoclaurine 6-O-methyltransferase
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 / acetylserotonin O-methyltransferase activity / melatonin biosynthetic process / alkaloid metabolic process / 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
: / (RS)-norcoclaurine 6-O-methyltransferase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5712
Polymers39,5321
Non-polymers391
Water91951
1
A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules

A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1424
Polymers79,0632
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8510 Å2
ΔGint-69 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.380, 99.310, 102.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

K

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Components

#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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: MPD, Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.7109 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7109 Å / Relative weight: 1
ReflectionResolution: 2.3→49.655 Å / Num. obs: 17348 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 45.587 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.71
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.41.1363.07199.5
2.4-2.60.6146.871100
2.6-2.90.26914.771100
2.9-3.30.10629.041100
3.3-4.30.05150.111100
4.3-6.30.03961.221100
6.3-9.30.03369.271100
9.30.02871.12199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
PHASERphasing
PHENIX1.5_2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICC

5icc


Resolution: 2.6→49.655 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.257 604 5 %
Rwork0.203 --
obs0.2058 12081 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 38.99 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 101.48 Å2 / Biso mean: 39.8286 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--4.0254 Å20 Å2-0 Å2
2--9.0183 Å20 Å2
3----4.9929 Å2
Refinement stepCycle: final / Resolution: 2.6→49.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 1 51 2545
Biso mean--25.29 27.28 -
Num. residues----323
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)
10.09350.0017-0.11230.3646-0.22131.63990.00250.031-0.0111-0.008-0.0701-0.0721-0.0313-0.34130.06460.090.0174-0.02340.1371-0.00920.0784-9.251512.202616.4411
20.384-0.02510.3350.0015-0.01490.28340.1436-0.0114-0.0327-0.3541-0.3096-0.0367-0.3299-0.22860.12580.210.3346-0.01890.058-0.00950.068514.4854-4.699524.4289
30.10040.15930.04080.43220.01761.0426-0.0550.0260.0088-0.0340.03970.12360.12010.130.01970.2255-0.03730.02860.10690.00740.129319.43229.47590.9599
40.2436-0.09710.70770.5755-0.27383.26370.25970.17230.1170.0355-0.08680.17560.15570.5511-0.12980.0559-0.01750.04990.14570.01080.094730.34713.408110.501
50.7947-0.1255-0.07220.89470.01250.29910.1637-0.09150.0609-0.055-0.12530.0086-0.03850.035-0.04310.1193-0.02810.01260.1033-0.00310.081613.89613.708619.9865
60.38980.3533-0.70641.7531-0.38021.3449-0.001-0.04810.029-0.01550.06710.2102-0.08020.3189-0.05080.1052-0.11230.01330.1426-0.02760.085628.109920.540813.073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:127)A8 - 127
2X-RAY DIFFRACTION2(chain A and resid 128:149)A128 - 149
3X-RAY DIFFRACTION3(chain A and resid 150:255)A150 - 255
4X-RAY DIFFRACTION4(chain A and resid 256:290)A256 - 290
5X-RAY DIFFRACTION5(chain A and resid 291:315)A291 - 315
6X-RAY DIFFRACTION6(chain A and resid 316:350)A316 - 350

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