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- PDB-6i73: Structure of Fragaria ananassa O-methyltransferase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6i73
TitleStructure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and protocatechuic aldehyde
ComponentsO-methyltransferase
KeywordsTRANSFERASE / fruit ripening / strawberry / volatiles / O-methyltransferase / SAM / SAH / caffeic acid / ferulic acid / protocatechuic aldehyde / vanillin / furaneol / furaneol methyl ether
Function / homology
Function and homology information


caffeate O-methyltransferase / lignin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / 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
Protocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE / caffeate O-methyltransferase
Similarity search - Component
Biological speciesFragaria ananassa (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHeldner, A. / Schiefner, A.
CitationJournal: To Be Published
Title: Structural insights into enzymatic formation of the strawberry flavor compound 2,5-dimethyl-4-methoxy-3(2H)-furanone
Authors: Heldner, A. / Schiefner, A.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,92212
Polymers79,4362
Non-polymers1,48510
Water17,961997
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-79 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.376, 87.655, 146.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein O-methyltransferase


Mass: 39718.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fragaria ananassa (strawberry) / Gene: omt1 / Plasmid: pASK75 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9M602

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Non-polymers , 5 types, 1007 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H6N / Protocatechuic aldehyde


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 997 / 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: 2.69 Å3/Da / Density % sol: 54.25 % / Description: bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M Ammonium sulfate, 1 M Lithium sulfate, 0.1 M Sodium malonate
PH range: 5.5-6.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2017
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.35→29.31 Å / Num. obs: 187792 / % possible obs: 100 % / Redundancy: 8.82 % / Biso Wilson estimate: 18.926 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.096 / Χ2: 1.11 / Net I/σ(I): 15.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.457.3730.8822.15358800.6910.9599.9
1.45-1.69.2720.4914.78384370.9350.52100
1.6-1.89.3260.2559.18334260.9810.271100
1.8-29.2910.1416.26214300.9930.148100
2-2.59.1260.0826.58282680.9970.085100
2.5-38.9850.05634.79126070.9980.06100
3-48.760.04142.59101090.9990.044100
4-68.720.03446.1253030.9990.036100
6-88.5920.03245.8213300.9990.034100
8-108.3460.0347.854860.9990.032100
10-29.315.9340.0339.985160.9990.03393.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KYW

1kyw


Resolution: 1.35→29.31 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.492 / SU ML: 0.026 / SU R Cruickshank DPI: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.148 3764 2 %RANDOM
Rwork0.1217 ---
obs0.1222 184027 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.35 Å2 / Biso mean: 15.123 Å2 / Biso min: 6.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2---0.56 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 1.35→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 103 1014 6515
Biso mean--14.79 27.41 -
Num. residues----706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0145949
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175541
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6668095
X-RAY DIFFRACTIONr_angle_other_deg1.1361.65212994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27623.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.698151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9981518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
X-RAY DIFFRACTIONr_rigid_bond_restr2.244311490
X-RAY DIFFRACTIONr_sphericity_free19.5225635
X-RAY DIFFRACTIONr_sphericity_bonded7.391511722
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 297 -
Rwork0.269 13435 -
all-13732 -
obs--99.84 %
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)
10.4408-0.09230.06750.8155-0.38440.658-0.0126-0.0082-0.0489-0.03890.03550.05280.0514-0.0319-0.0230.005-0.0024-0.00060.0499-0.0040.0086-2.2327-34.416318.053
22.3580.8671-0.97341.6193-0.52352.4243-0.0155-0.03350.05080.03290.00050.1809-0.0748-0.2410.0150.02210.0266-0.01010.0855-0.00310.0372-21.7631-12.32528.963
30.9222-0.13490.43040.5119-0.11411.0206-0.0124-0.04590.11780.0282-0.00140.0099-0.1554-0.06280.01390.03680.01130.00290.0358-0.00870.0203-7.9138-8.051717.9327
42.12531.3733-0.3563.86-1.04481.89120.0211-0.13420.25880.27920.02540.2521-0.3015-0.176-0.04650.11180.04030.00180.0805-0.02950.0546-14.5569-2.211722.7216
50.5379-0.3555-0.18160.75620.15590.435-0.0272-0.0850.04010.05230.0246-0.0906-0.02140.07030.00260.0089-0.0124-0.00910.07040.00490.012515.4502-26.600624.7802
62.66020.91062.59852.26952.03628.2403-0.03390.0083-0.03310.00890.0188-0.3124-0.16660.33710.01510.00940.00850.00270.13050.02420.115536.1345-43.622825.0976
71.6891-0.3317-0.20270.6280.06390.8025-0.0216-0.1244-0.18520.0572-0.0133-0.04610.11460.12890.03490.03530.01590.00620.070.03580.048620.9398-50.28126.7587
84.59060.2878-0.12516.88940.85678.2844-0.151-0.5548-0.56440.740.163-0.15510.72750.2481-0.0120.15370.05890.0170.16170.07230.169126.9824-61.827334.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 187
2X-RAY DIFFRACTION2A188 - 258
3X-RAY DIFFRACTION3A259 - 331
4X-RAY DIFFRACTION4A332 - 365
5X-RAY DIFFRACTION5B13 - 217
6X-RAY DIFFRACTION6B218 - 238
7X-RAY DIFFRACTION7B239 - 360
8X-RAY DIFFRACTION8B361 - 365

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