[English] 日本語
Yorodumi
- PDB-8xdy: O-methyltransferase from Lycoris longituba M52A variant complexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xdy
TitleO-methyltransferase from Lycoris longituba M52A variant complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde
Componentsnorbelladine O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase family protein / LlOMT
Function / homology
Function and homology information


norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE / norbelladine O-methyltransferase
Similarity search - Component
Biological speciesLycoris longituba (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: norbelladine O-methyltransferase
B: norbelladine O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02810
Polymers54,7662
Non-polymers1,2628
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-32 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.857, 81.492, 117.872
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 norbelladine O-methyltransferase


Mass: 27383.229 Da / Num. of mol.: 2 / Mutation: M52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycoris longituba (plant) / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A6B9TNK2

-
Non-polymers , 6 types, 244 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.: 236 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
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: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 2.2→47.76 Å / Num. obs: 46990 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 31.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2173 / CC1/2: 0.842 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.76 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.7259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 2379 5.06 %
Rwork0.1779 44611 -
obs0.1791 46990 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 24 236 4122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264160
X-RAY DIFFRACTIONf_angle_d0.61695672
X-RAY DIFFRACTIONf_chiral_restr0.0438627
X-RAY DIFFRACTIONf_plane_restr0.0034735
X-RAY DIFFRACTIONf_dihedral_angle_d19.47031554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.31771310.28182625X-RAY DIFFRACTION100
2.24-2.290.28681250.25372641X-RAY DIFFRACTION99.86
2.29-2.350.24931190.24192651X-RAY DIFFRACTION99.89
2.35-2.410.23061360.24132646X-RAY DIFFRACTION99.78
2.41-2.470.22541390.22472625X-RAY DIFFRACTION99.78
2.47-2.540.28331420.2242599X-RAY DIFFRACTION99.6
2.54-2.630.24851360.20232644X-RAY DIFFRACTION99.46
2.63-2.720.22661560.19482580X-RAY DIFFRACTION99.09
2.72-2.830.26651520.19572576X-RAY DIFFRACTION99.38
2.83-2.960.20131370.19832642X-RAY DIFFRACTION99.86
2.96-3.110.25291160.18532676X-RAY DIFFRACTION99.86
3.11-3.310.19721550.16742605X-RAY DIFFRACTION100
3.31-3.560.17651590.1652631X-RAY DIFFRACTION100
3.56-3.920.17761350.14262590X-RAY DIFFRACTION100
3.92-4.490.14131320.12732657X-RAY DIFFRACTION100
4.49-5.650.17071660.15242603X-RAY DIFFRACTION100
5.65-47.760.18151430.17342620X-RAY DIFFRACTION99.57
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)
10.679220805149-0.02735651271230.3303934800470.2886527886590.09472230990571.163093120640.03443090520390.000811732055843-0.0358504256329-0.120241068431-0.01397420534180.0004723704147610.0162416595789-0.1329211081514.01118753816E-60.241220701975-0.000197113161023-0.002337454133220.2525676457980.006163255984050.23394901353-2.2783459062410.652979325920.3534413431
20.3129923055160.05703123477770.2444624382020.220177352977-0.3132619850020.797596927796-0.09287656100520.0795490549070.182476186916-0.278386054030.06783122952480.0756902262182-0.249684135433-0.00562051603884-3.21105485171E-50.378723953752-0.008792698491550.01047265850080.2724313293540.007146701259570.289984810813.9865429348821.70010386768.30395377
30.335582845199-0.06296528161130.1968395651770.0778678053755-0.2023607004720.5439695620580.03415522869480.075326013575-0.0837643092091-0.178091865312-0.00392960535711-0.07483001838510.07836725189160.114020760349-1.70407092304E-50.244470301964-0.01049628484730.06426601254110.231842672338-0.04113657046010.27007601874113.50819169855.308726535614.4498285985
40.4148435828930.3159353226860.1402393575970.3925657395960.2387296716180.176895989483-0.0140218187896-0.216812694093-0.3458497973580.197291680697-0.040073981714-0.1867043576790.2610155745120.2071479426591.42826905899E-50.355209175860.0262116502195-0.02315717119310.3268027180860.04363129391610.40695785550315.2433335119-2.5759627647535.5574510683
50.1274652793560.06922686032150.1380447900360.1671360563660.05658705706780.1491040989980.00721696512562-0.124489967254-0.2171885780430.09045915943610.154622617676-0.0344182934750.2843870828510.3431819157757.56675067751E-50.3442528621440.0352828542108-0.02891972073920.3156024432850.0007345836252190.39687971802125.26257488910.87179843027940.3305862455
60.462862810947-0.43470048032-0.03426748637480.4006659646180.07615955727270.4341804664780.0290712076928-0.09949756407740.04069332420870.16064173944-0.040753253768-0.251314991061-0.08939943753430.1891063936418.47002342272E-60.251002425479-0.0514575629494-0.03390288341010.296066749821-0.02554046294180.31060162250422.552892627417.822484020141.660724041
70.5058444253970.07902914716070.4469905874430.3706485823310.328125485160.934682693163-0.0146010500007-0.1128302477650.001843948747280.08520614077530.0643952576897-0.0144289727407-0.039787886489-0.1052323851978.4454887729E-60.2173217928550.004817669289110.005545724545250.2243760926920.00288601515890.1898733511674.724160967413.682880082542.1526520558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 239 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 35 )
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 56 )
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 157 )
7X-RAY DIFFRACTION7chain 'B' and (resid 158 through 239 )

+
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