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- PDB-6i71: Structure of Fragaria ananassa O-methyltransferase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6i71
TitleStructure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine
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


lignin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / Plant 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / Plant 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-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 / O-methyltransferase
Similarity search - Component
Biological speciesFragaria ananassa (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,77012
Polymers79,4362
Non-polymers1,33310
Water15,943885
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-69 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.387, 87.772, 145.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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 (E. coli) / Strain (production host): BL21 / References: UniProt: Q9M602
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 885 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.8 % / Description: bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5-1 M Ammonium sulfate, 1 M Lithium sulfate, 0.1 M Sodium malonate
PH range: 5.0-6.5

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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: 1.4→29.96 Å / Num. obs: 164879 / % possible obs: 98.7 % / Redundancy: 8.893 % / Biso Wilson estimate: 22.165 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 1.022 / Net I/σ(I): 22.69 / Num. measured all: 1466233 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.57.1880.7582.4288160.7630.81793.2
1.5-1.69.2750.4495.01236990.9350.475100
1.6-1.89.3270.2349.46330700.9830.248100
1.8-29.3540.11119.2212440.9960.117100
2-2.59.3270.05536.35280200.9990.058100
2.5-39.2390.03751.42124550.9990.039100
3-49.030.02864.66100140.9990.03100
4-68.9370.02370.58524610.025100
6-88.6630.02268.41132310.024100
8-108.320.01971.6348510.02100
10-29.965.7810.02159.845070.9990.02393.7

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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: 6I73

6i73


Resolution: 1.4→29.96 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.745 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0471 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 3319 2 %RANDOM
Rwork0.1505 ---
obs0.1508 161560 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.6 Å2 / Biso mean: 19.185 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20 Å2
2--0.46 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 86 902 6386
Biso mean--20.63 30.47 -
Num. residues----706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0145840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175439
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6617941
X-RAY DIFFRACTIONr_angle_other_deg1.0951.65412751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6524.388237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.521151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1651514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021053
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 193 -
Rwork0.292 10480 -
all-10673 -
obs--87.33 %
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)
11.4775-0.18920.07641.1926-0.15911.2222-0.02-0.0165-0.1331-0.01830.0225-0.07330.17450.0964-0.00250.02560.01390.00270.0158-0.00690.02470.7877-0.1804-19.7711
20.01060.07350.02791.39390.37380.11890.0534-0.0305-0.03060.5-0.0355-0.12670.2036-0.0342-0.01790.4524-0.03840.02180.34310.01120.42342.0122-18.8298-26.7892
30.75760.27530.12041.01020.13710.5259-0.01040.05580.0558-0.08010.0113-0.06-0.10840.1467-0.00090.0306-0.01810.0020.0636-0.00490.015410.650328.1641-15.2593
40.83140.2999-0.13250.7539-0.17860.9981-0.03830.07710.0955-0.0470.03390.0636-0.081-0.05570.00440.01530.0063-0.0120.0232-0.00030.0178-12.716517.9452-22.7396
52.32450.2730.31470.9028-0.291.1361-0.02830.1074-0.1267-0.07810.03380.04580.0967-0.1597-0.00550.0191-0.01950.00270.0466-0.02820.0383-26.3265-6.1251-23.5061
62.323-0.328-0.4242.581-0.16252.327-0.09320.3351-0.4506-0.39490.024-0.09060.4098-0.0450.06920.1322-0.02930.03120.0714-0.07390.13-21.2929-14.602-28.2264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 93
2X-RAY DIFFRACTION2A94 - 103
3X-RAY DIFFRACTION3A104 - 401
4X-RAY DIFFRACTION4B13 - 182
5X-RAY DIFFRACTION5B183 - 331
6X-RAY DIFFRACTION6B332 - 401

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