[English] 日本語
Yorodumi
- PDB-7v6l: LcCOMT in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v6l
TitleLcCOMT in complex with SAH
ComponentsLcCOMT
KeywordsTRANSFERASE / SAM / complex
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesLigusticum chuanxiong (chuang-xiong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsYu, Y. / CHen, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism.
Authors: Song, S. / Chen, A. / Zhu, J. / Yan, Z. / An, Q. / Zhou, J. / Liao, H. / Yu, Y.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LcCOMT
B: LcCOMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6774
Polymers79,9082
Non-polymers7692
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-75 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.393, 60.169, 129.901
Angle α, β, γ (deg.)90.000, 95.260, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LcCOMT


Mass: 39954.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ligusticum chuanxiong (chuang-xiong) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 51456 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rrim(I) all: 0.129 / Net I/σ(I): 14
Reflection shellResolution: 1.948→2 Å / Num. unique obs: 3108 / CC1/2: 0.939

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3reo

3reo


Resolution: 1.948→44.053 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2193 4.96 %
Rwork0.1923 41980 -
obs0.1943 44173 84.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.42 Å2 / Biso mean: 27.3956 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: final / Resolution: 1.948→44.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 90 329 5751
Biso mean--20.62 24.64 -
Num. residues----691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9481-1.99050.2428660.2257154350
1.9905-2.03680.2931060.2341181759
2.0368-2.08770.2851050.2246195163
2.0877-2.14420.27561120.2141209168
2.1442-2.20730.26351280.2123220271
2.2073-2.27850.25231250.2078236777
2.2785-2.35990.23961400.2198255283
2.3599-2.45440.24251440.2115272087
2.4544-2.56610.25321520.2099289994
2.5661-2.70140.24491550.2159306999
2.7014-2.87060.2671660.20293080100
2.8706-3.09220.23661670.20633101100
3.0922-3.40330.24881650.19093097100
3.4033-3.89550.21141550.17653126100
3.8955-4.90680.18181440.15133150100
4.9068-44.0530.20741630.17463215100

+
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