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- PDB-6i70: Structure of Fragaria ananassa O-methyltransferase - apo form -

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Basic information

Entry
Database: PDB / ID: 6i70
TitleStructure of Fragaria ananassa O-methyltransferase - apo form
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
NITRATE ION / caffeate O-methyltransferase
Similarity search - Component
Biological speciesFragaria ananassa (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)79,5604
Polymers79,4362
Non-polymers1242
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-69 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.203, 147.098, 131.057
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 14 - 364 / Label seq-ID: 11 - 361

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 BL21 (bacteria) / References: UniProt: Q9M602
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.25 Å3/Da / Density % sol: 45.36 % / Description: cuboid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30 % (w/v) PEG3350, 0.2 M Lithium nitrate, 0.1 M Hepes/Sodium
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 30, 2017
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→34.73 Å / Num. obs: 42203 / % possible obs: 99.9 % / Redundancy: 10.45 % / Biso Wilson estimate: 50.056 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.065 / Χ2: 1.002 / Net I/σ(I): 24.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.210.1291.2671.8954300.7071.336100
2.2-2.310.720.7123.4645330.8920.748100
2.3-2.510.9710.3926.3170520.9680.412100
2.5-310.4330.15614.5104620.9950.164100
3-410.4910.04641.8583970.9990.049100
4-69.8910.02768.01440110.029100
6-810.0980.02471.84109110.025100
8-1010.7070.0287.0540610.022100
10-34.739.0530.02477.0843110.02596

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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: 2.1→34.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.463 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2418 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2138 5.1 %RANDOM
Rwork0.2021 ---
obs0.2034 40065 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.55 Å2 / Biso mean: 54.529 Å2 / Biso min: 26.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.1→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 8 173 5551
Biso mean--68.66 48.14 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0145522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175170
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6437480
X-RAY DIFFRACTIONr_angle_other_deg0.9251.63912095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67624.141227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9215961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2641514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
Refine LS restraints NCS

Ens-ID: 1 / Number: 10547 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 157 -
Rwork0.425 2930 -
all-3087 -
obs--100 %
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)
15.68642.33070.08410.95960.03990.0209-0.15020.07150.0621-0.06630.05740.0578-0.0124-0.01530.09280.3776-0.0217-0.00160.37330.00380.4481-33.3908-62.112-10.1132
21.87320.3083-0.38254.007-0.24773.2835-0.42840.64440.2485-1.110.23150.2579-0.1298-0.33380.19690.4288-0.1234-0.1490.31330.05640.0715-23.9784-43.8396-31.2732
32.59550.07280.09221.9164-0.56111.4245-0.12810.01440.1110.00990.0809-0.0725-0.35080.15680.04720.1606-0.0199-0.04960.1243-0.01240.0319-7.9746-35.7303-12.0077
41.08650.7616-0.08945.3633-0.24351.69210.1270.03760.402-0.1081-0.2064-0.0692-0.58830.17680.07940.29180.00250.01410.17690.0110.1864-19.0653-18.0993-4.5807
54.43670.3344-0.44067.46980.77096.4384-0.0218-0.24430.44230.3266-0.11870.509-0.408-0.26590.14050.1671-0.03330.06630.1187-0.03280.1677-25.4356-23.10823.7262
61.51460.5549-0.63792.65070.55573.4144-0.159-0.07450.00410.07010.0324-0.07180.28180.04410.12660.06010.0183-0.00210.0547-0.00680.0121-18.6739-49.8991-4.5939
74.7885-3.3502-3.82493.46994.9838.14870.44480.0139-1.05750.17240.8952-0.47941.18341.7723-1.341.10570.3657-0.13730.7877-0.83461.9003-0.4816-57.57-23.2607
82.9001-0.46651.18553.6513-1.193.4556-0.14780.0975-0.4407-0.30860.1073-0.16220.32250.05460.04060.344-0.06650.17880.1825-0.0610.1436-15.5346-76.7139-24.9169
96.10080.9251-3.23073.993-0.00694.26580.0872-0.0384-0.0388-0.1049-0.01160.141-0.05910.0335-0.07570.227-0.0547-0.03270.1895-0.00930.1093-22.9056-55.1713-24.5189
103.9837-0.81250.43058.53530.30935.6252-0.22650.0996-0.3143-0.22260.23160.80680.2991-0.3781-0.00510.2839-0.08140.00840.31-0.04260.1235-26.1515-71.2497-32.5966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 19
2X-RAY DIFFRACTION2A20 - 119
3X-RAY DIFFRACTION3A120 - 183
4X-RAY DIFFRACTION4A184 - 323
5X-RAY DIFFRACTION5A324 - 364
6X-RAY DIFFRACTION6B14 - 154
7X-RAY DIFFRACTION7B155 - 171
8X-RAY DIFFRACTION8B172 - 303
9X-RAY DIFFRACTION9B304 - 324
10X-RAY DIFFRACTION10B325 - 364

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