[English] 日本語
Yorodumi
- PDB-8xdr: O-methyltransferase from Lycoris aurea complexed with Mg, SAH, an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xdr
TitleO-methyltransferase from Lycoris aurea complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / O-methyltransferase family protein / LaOMT
Function / homologyProtocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesLycoris aurea (golden spider-lily)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSaw, Y.Y.H. / Nakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H02777 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15303 Japan
CitationJournal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.
History
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,10810
Polymers54,8472
Non-polymers1,2628
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-33 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.373, 81.091, 116.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein O-methyltransferase family protein


Mass: 27423.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycoris aurea (golden spider-lily) / Production host: Escherichia coli M15 (bacteria)

-
Non-polymers , 6 types, 387 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-H6N / Protocatechuic aldehyde


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.048 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.048 Å / Relative weight: 1
ReflectionResolution: 1.83→47.38 Å / Num. obs: 78525 / % possible obs: 98.6 % / Redundancy: 8.3 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2469 / CC1/2: 0.735

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→47.38 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 21.0378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 3949 5.03 %
Rwork0.1665 74576 -
obs0.1684 78525 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.42 Å2
Refinement stepCycle: LAST / Resolution: 1.83→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 8 379 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01014076
X-RAY DIFFRACTIONf_angle_d1.03755553
X-RAY DIFFRACTIONf_chiral_restr0.0613622
X-RAY DIFFRACTIONf_plane_restr0.0061712
X-RAY DIFFRACTIONf_dihedral_angle_d16.9933589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.31911600.28622569X-RAY DIFFRACTION97.01
1.85-1.880.29161340.2762627X-RAY DIFFRACTION97.39
1.88-1.90.32321510.26792703X-RAY DIFFRACTION97.71
1.9-1.930.27531340.2482607X-RAY DIFFRACTION97.2
1.93-1.950.31851590.24052628X-RAY DIFFRACTION97.82
1.95-1.980.29521450.23382655X-RAY DIFFRACTION97.56
1.98-2.010.28271240.2212652X-RAY DIFFRACTION97.88
2.01-2.050.22981370.2012659X-RAY DIFFRACTION98.07
2.05-2.080.25891700.19372617X-RAY DIFFRACTION97.62
2.08-2.120.2231260.18392691X-RAY DIFFRACTION98.22
2.12-2.160.20411220.1742685X-RAY DIFFRACTION98.28
2.16-2.210.22691530.18242632X-RAY DIFFRACTION98.03
2.21-2.250.22541610.1762655X-RAY DIFFRACTION97.88
2.25-2.310.20851300.16752658X-RAY DIFFRACTION98.48
2.31-2.360.21381380.1652683X-RAY DIFFRACTION98.67
2.36-2.430.22011340.16522683X-RAY DIFFRACTION98.67
2.43-2.50.22421210.17352673X-RAY DIFFRACTION98.45
2.5-2.580.22231350.16672657X-RAY DIFFRACTION98.21
2.58-2.670.22641290.16432632X-RAY DIFFRACTION97.29
2.67-2.780.2011280.16862713X-RAY DIFFRACTION98.13
2.78-2.90.21591240.1742708X-RAY DIFFRACTION98.68
2.9-3.060.21211360.16812671X-RAY DIFFRACTION99.4
3.06-3.250.19591370.15352700X-RAY DIFFRACTION98.95
3.25-3.50.19551650.14112676X-RAY DIFFRACTION99.3
3.5-3.850.16891810.13722653X-RAY DIFFRACTION99.26
3.85-4.410.13961450.12472656X-RAY DIFFRACTION99.61
4.41-5.550.16711470.13442722X-RAY DIFFRACTION99.69
5.55-47.380.18581230.17352711X-RAY DIFFRACTION99.44

+
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