[English] 日本語
Yorodumi
- PDB-5x1m: Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x1m
TitleVanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-tetrahydrofolate complex form
ComponentsVanillate/3-O-methylgallate O-demethylase
KeywordsOXIDOREDUCTASE / Lignin / Sphingobium sp. SYK-6
Function / homology
Function and homology information


vanillate/3-O-methylgallate O-demethylase / lignin catabolic process / methyltransferase activity / methylation
Similarity search - Function
Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / (6S)-5,6,7,8-TETRAHYDROFOLATE / Vanillate/3-O-methylgallate O-demethylase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarada, A. / Senda, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science14J04356 Japan
the Ministry of Education, Culture, Sports, Science and TechnologyPlatform for Drug Discovery, Informatics, and Structural Life Science Japan
Japan Agency for Medical Research and Development (AMED)Platform for Drug Discovery, Informatics, and Structural Life Science Japan
CitationJournal: FEBS J. / Year: 2017
Title: The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6
Authors: Harada, A. / Kamimura, N. / Takeuchi, K. / Yu, H.Y. / Masai, E. / Senda, T.
History
DepositionJan 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vanillate/3-O-methylgallate O-demethylase
B: Vanillate/3-O-methylgallate O-demethylase
C: Vanillate/3-O-methylgallate O-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,89414
Polymers157,8363
Non-polymers2,05811
Water5,909328
1
A: Vanillate/3-O-methylgallate O-demethylase
hetero molecules

A: Vanillate/3-O-methylgallate O-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,32910
Polymers105,2242
Non-polymers1,1058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6250 Å2
ΔGint-2 kcal/mol
Surface area32470 Å2
MethodPISA
2
B: Vanillate/3-O-methylgallate O-demethylase
C: Vanillate/3-O-methylgallate O-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7309
Polymers105,2242
Non-polymers1,5057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-6 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.802, 118.370, 132.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Vanillate/3-O-methylgallate O-demethylase


Mass: 52612.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligM, SLG_12740 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2IQS7

-
Non-polymers , 5 types, 339 molecules

#2: Chemical
ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.45 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 0.1M LiCl, 25%(w/v) PEG8000

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2015
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.32 Å / Num. obs: 257350 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 14.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X1I

5x1i


Resolution: 1.9→47.533 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.48
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2423 12140 4.89 %
Rwork0.2082 --
obs0.2099 248062 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10492 0 144 328 10964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611009
X-RAY DIFFRACTIONf_angle_d0.89715035
X-RAY DIFFRACTIONf_dihedral_angle_d14.4756400
X-RAY DIFFRACTIONf_chiral_restr0.0551590
X-RAY DIFFRACTIONf_plane_restr0.0071953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.38694170.36577859X-RAY DIFFRACTION100
1.9216-1.94420.37634060.34167862X-RAY DIFFRACTION100
1.9442-1.96790.3834060.33357855X-RAY DIFFRACTION100
1.9679-1.99280.34114400.31297840X-RAY DIFFRACTION100
1.9928-2.01910.35134150.31037825X-RAY DIFFRACTION100
2.0191-2.04670.34863920.29417889X-RAY DIFFRACTION100
2.0467-2.0760.30284030.28817913X-RAY DIFFRACTION100
2.076-2.10690.28894100.26957812X-RAY DIFFRACTION100
2.1069-2.13990.31653920.25547849X-RAY DIFFRACTION100
2.1399-2.17490.33773480.25547918X-RAY DIFFRACTION100
2.1749-2.21240.30493910.2427929X-RAY DIFFRACTION100
2.2124-2.25270.27314130.24017851X-RAY DIFFRACTION100
2.2527-2.2960.28464320.23617815X-RAY DIFFRACTION100
2.296-2.34290.25883800.21917893X-RAY DIFFRACTION100
2.3429-2.39380.27823500.2277873X-RAY DIFFRACTION100
2.3938-2.44950.2984160.23167889X-RAY DIFFRACTION100
2.4495-2.51070.24784450.22537862X-RAY DIFFRACTION100
2.5107-2.57860.31813900.24487860X-RAY DIFFRACTION100
2.5786-2.65450.26133890.23867898X-RAY DIFFRACTION100
2.6545-2.74020.30834020.24237866X-RAY DIFFRACTION100
2.7402-2.83810.26813690.2397819X-RAY DIFFRACTION100
2.8381-2.95170.25854230.23377901X-RAY DIFFRACTION100
2.9517-3.0860.27594550.23117811X-RAY DIFFRACTION100
3.086-3.24870.22634050.21557867X-RAY DIFFRACTION100
3.2487-3.45220.2394000.19767863X-RAY DIFFRACTION100
3.4522-3.71860.22324160.18017851X-RAY DIFFRACTION100
3.7186-4.09270.19323810.16627913X-RAY DIFFRACTION100
4.0927-4.68440.17014040.13547872X-RAY DIFFRACTION100
4.6844-5.90010.16064440.13997798X-RAY DIFFRACTION100
5.9001-47.54750.15634060.14727869X-RAY DIFFRACTION100

+
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