[English] 日本語
Yorodumi
- PDB-8qfn: Ergothioneine dioxygenase from Thermocatellispora tengchongensis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qfn
TitleErgothioneine dioxygenase from Thermocatellispora tengchongensis in complex with manganese and in presence of catalase aerobic
ComponentsCysteine dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase Ergothioneine Dioxygenase
Function / homologyCysteine dioxygenase type I / Cysteine dioxygenase type I / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / ferrous iron binding / ACETATE ION / : / Cysteine dioxygenase
Function and homology information
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVasseur, C.M. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182023 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Enzyme-Catalyzed Oxidative Degradation of Ergothioneine.
Authors: Nalivaiko, E.Y. / Vasseur, C.M. / Seebeck, F.P.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine dioxygenase
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03511
Polymers41,4082
Non-polymers6279
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-26 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.507, 59.209, 134.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cysteine dioxygenase


Mass: 20704.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocatellispora tengchongensis (bacteria)
Gene: HNP84_002159 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A840P3H4

-
Non-polymers , 6 types, 210 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate 0.1 M sodium cacodylate, pH 6.5 20% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→44.51 Å / Num. obs: 72960 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 13.89
Reflection shellResolution: 1.75→1.813 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7181 / CC1/2: 0.727

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→44.45 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 3431 4.98 %
Rwork0.1875 --
obs0.1893 68859 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 36 201 2665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052523
X-RAY DIFFRACTIONf_angle_d0.7993417
X-RAY DIFFRACTIONf_dihedral_angle_d20.621350
X-RAY DIFFRACTIONf_chiral_restr0.052350
X-RAY DIFFRACTIONf_plane_restr0.004452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.36121470.36212632X-RAY DIFFRACTION99
1.77-1.80.36371510.33732573X-RAY DIFFRACTION99
1.8-1.830.35311250.31732605X-RAY DIFFRACTION99
1.83-1.850.3251450.3122635X-RAY DIFFRACTION98
1.85-1.890.3781350.2892530X-RAY DIFFRACTION98
1.89-1.920.28961190.27332652X-RAY DIFFRACTION99
1.92-1.950.29491440.25352622X-RAY DIFFRACTION99
1.95-1.990.31431470.22622597X-RAY DIFFRACTION100
1.99-2.030.23751430.20962626X-RAY DIFFRACTION100
2.03-2.070.22371490.19972593X-RAY DIFFRACTION100
2.07-2.120.25581530.20422664X-RAY DIFFRACTION100
2.12-2.180.21691190.19462638X-RAY DIFFRACTION100
2.18-2.230.24891520.19112597X-RAY DIFFRACTION100
2.24-2.30.24121310.18442619X-RAY DIFFRACTION100
2.3-2.380.25731320.1782666X-RAY DIFFRACTION100
2.38-2.460.25251290.17992638X-RAY DIFFRACTION100
2.46-2.560.20791140.17332648X-RAY DIFFRACTION100
2.56-2.670.23371530.17032498X-RAY DIFFRACTION96
2.67-2.820.20131290.15822652X-RAY DIFFRACTION100
2.82-2.990.17521000.17082657X-RAY DIFFRACTION100
2.99-3.220.19791520.17072629X-RAY DIFFRACTION100
3.22-3.550.20161340.17072632X-RAY DIFFRACTION100
3.55-4.060.17231560.15992630X-RAY DIFFRACTION100
4.06-5.110.18681360.14922559X-RAY DIFFRACTION98
5.12-44.450.2481360.1972636X-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