[English] 日本語
Yorodumi
- PDB-8c9t: Catechol O-methyltransferase from Streptomyces avermitilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c9t
TitleCatechol O-methyltransferase from Streptomyces avermitilis
ComponentsPutative O-methyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


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
Biological speciesStreptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhang, L. / Groves, M.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)893122European Union
CitationJournal: Chembiochem / Year: 2023
Title: Structural Characterization and Extended Substrate Scope Analysis of Two Mg 2+ -Dependent O-Methyltransferases from Bacteria.
Authors: Sokolova, N. / Zhang, L. / Deravi, S. / Oerlemans, R. / Groves, M.R. / Haslinger, K.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative O-methyltransferase
B: Putative O-methyltransferase
C: Putative O-methyltransferase
D: Putative O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0456
Polymers100,8614
Non-polymers1842
Water12,827712
1
A: Putative O-methyltransferase
D: Putative O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5233
Polymers50,4312
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-34 kcal/mol
Surface area17780 Å2
MethodPISA
2
B: Putative O-methyltransferase
C: Putative O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5233
Polymers50,4312
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-37 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.457, 168.744, 57.242
Angle α, β, γ (deg.)90.000, 101.487, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative O-methyltransferase


Mass: 25215.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
Gene: SAVERM_5837 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82B68
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MIB(Malonic acid,Imidazole,Boric acid) pH6.0; 25% PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→46.71 Å / Num. obs: 131969 / % possible obs: 96.2 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.278 / Num. unique obs: 5286 / CC1/2: 0.967

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.093 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1936 6583 4.99 %
Rwork0.1669 125335 -
all0.168 --
obs-131918 96.071 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.356 Å2-0 Å2-0.445 Å2
2---0.57 Å20 Å2
3---1.023 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 12 712 7483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136987
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156719
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.6379531
X-RAY DIFFRACTIONr_angle_other_deg1.5631.58115456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89321.23374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.487151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.671564
X-RAY DIFFRACTIONr_chiral_restr0.0890.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021558
X-RAY DIFFRACTIONr_nbd_refined0.2250.21514
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26572
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23499
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2520
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.234
X-RAY DIFFRACTIONr_nbd_other0.2150.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.255
X-RAY DIFFRACTIONr_mcbond_it1.421.3043594
X-RAY DIFFRACTIONr_mcbond_other1.4111.3033593
X-RAY DIFFRACTIONr_mcangle_it2.0531.9524497
X-RAY DIFFRACTIONr_mcangle_other2.0551.9534498
X-RAY DIFFRACTIONr_scbond_it2.4351.6133393
X-RAY DIFFRACTIONr_scbond_other2.4351.6133394
X-RAY DIFFRACTIONr_scangle_it3.6842.3075025
X-RAY DIFFRACTIONr_scangle_other3.6832.3085026
X-RAY DIFFRACTIONr_lrange_it4.65517.1728020
X-RAY DIFFRACTIONr_lrange_other4.65417.1748021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2394640.27899X-RAY DIFFRACTION82.622
1.539-1.5810.2034590.1768818X-RAY DIFFRACTION94.0777
1.581-1.6270.2044480.1698712X-RAY DIFFRACTION95.5261
1.627-1.6770.24300.1698658X-RAY DIFFRACTION96.9697
1.677-1.7320.2084390.1658410X-RAY DIFFRACTION97.2845
1.732-1.7930.2024110.1648103X-RAY DIFFRACTION96.9373
1.793-1.860.1974240.1637723X-RAY DIFFRACTION96.9765
1.86-1.9360.2044020.1587333X-RAY DIFFRACTION94.9313
1.936-2.0230.1753430.1697300X-RAY DIFFRACTION97.9872
2.023-2.1210.1933660.1627003X-RAY DIFFRACTION98.4239
2.121-2.2360.1953360.1666611X-RAY DIFFRACTION98.5949
2.236-2.3720.2053610.1636265X-RAY DIFFRACTION98.4108
2.372-2.5350.2023180.1615873X-RAY DIFFRACTION98.3323
2.535-2.7380.1852780.1595307X-RAY DIFFRACTION94.4529
2.738-30.1812480.1625104X-RAY DIFFRACTION99.4796
3-3.3540.2032460.174636X-RAY DIFFRACTION99.6123
3.354-3.8720.1712150.1584106X-RAY DIFFRACTION99.6081
3.872-4.7420.1731750.1523435X-RAY DIFFRACTION98.8229
4.742-6.7030.2171250.2172575X-RAY DIFFRACTION95.4738

+
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