[English] 日本語
Yorodumi
- PDB-6i73: Structure of Fragaria ananassa O-methyltransferase in complex wit... -

+
Open data


ID or keywords:

Loading...

-
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 / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / 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 / 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
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
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 1007 molecules

#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-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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more