[English] 日本語
Yorodumi
- PDB-8qf6: Sulfoxide synthase from Chloracidobacterium thermophilum, EgtB ty... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qf6
TitleSulfoxide synthase from Chloracidobacterium thermophilum, EgtB type II, in complex with iron and trimethylhistidine
ComponentsErgothioneine biosynthesis protein EgtB
KeywordsOXIDOREDUCTASE / EgtB Ergothioneine isoTMH
Function / homology
Function and homology information


ergothioneine biosynthetic process / metal ion binding
Similarity search - Function
Ergothioneine biosynthesis protein EgtB / DinB-like domain / DinB superfamily / DinB/YfiT-like putative metalloenzymes / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold
Similarity search - Domain/homology
: / : / Ergothioneine biosynthesis protein EgtB
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVasseur, C.M. / Stampfli, A.R. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182023 Switzerland
CitationJournal: To Be Published
Title: Catalytic mechanism analysis of sulfoxide synthase via inhibition assay
Authors: Vasseur, C.M. / Stampfli, A.R. / Seebeck, F.P.
History
DepositionSep 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ergothioneine biosynthesis protein EgtB
B: Ergothioneine biosynthesis protein EgtB
C: Ergothioneine biosynthesis protein EgtB
D: Ergothioneine biosynthesis protein EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,64512
Polymers196,6334
Non-polymers1,0128
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.708, 124.439, 90.055
Angle α, β, γ (deg.)90.00, 112.05, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ergothioneine biosynthesis protein EgtB


Mass: 49158.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: Cabther_A1318
Production host: Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LET6
#2: Chemical
ChemComp-UCQ / (2~{S})-2-(dimethylamino)-3-(3-methylimidazol-4-yl)propanoic acid


Mass: 197.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M zinc acetate dehydrate, 20% w/v polyethylene glycol 3350, pH 6.4

-
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: Oct 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.88 Å / Num. obs: 4333932 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.997 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 21960 / CC1/2: 0.614

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.88 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 4415 5.04 %
Rwork0.1888 --
obs0.1913 87591 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12809 0 60 592 13461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913352
X-RAY DIFFRACTIONf_angle_d1.06818257
X-RAY DIFFRACTIONf_dihedral_angle_d17.8441833
X-RAY DIFFRACTIONf_chiral_restr0.0581853
X-RAY DIFFRACTIONf_plane_restr0.0072409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.35981440.26892805X-RAY DIFFRACTION100
2.23-2.250.35751460.30712732X-RAY DIFFRACTION100
2.25-2.280.41071330.30982764X-RAY DIFFRACTION99
2.28-2.310.3591570.28322763X-RAY DIFFRACTION100
2.31-2.340.33371520.24932740X-RAY DIFFRACTION100
2.34-2.370.321590.2472747X-RAY DIFFRACTION100
2.37-2.40.29451550.23742747X-RAY DIFFRACTION100
2.4-2.440.32621630.24732780X-RAY DIFFRACTION100
2.44-2.480.32561460.23892742X-RAY DIFFRACTION100
2.48-2.520.32051520.23912772X-RAY DIFFRACTION100
2.52-2.560.27731380.22522768X-RAY DIFFRACTION100
2.56-2.610.26871210.21632761X-RAY DIFFRACTION100
2.61-2.660.30681470.21432804X-RAY DIFFRACTION100
2.66-2.710.28321210.21382771X-RAY DIFFRACTION100
2.71-2.770.26161380.19852771X-RAY DIFFRACTION100
2.77-2.840.28241550.21352776X-RAY DIFFRACTION100
2.84-2.910.25671650.21332744X-RAY DIFFRACTION100
2.91-2.990.24941670.20492734X-RAY DIFFRACTION100
2.99-3.070.24271450.19822795X-RAY DIFFRACTION100
3.07-3.170.25591390.19522768X-RAY DIFFRACTION100
3.17-3.290.25221490.19132770X-RAY DIFFRACTION100
3.29-3.420.23861370.18922792X-RAY DIFFRACTION100
3.42-3.570.24251430.18382772X-RAY DIFFRACTION100
3.57-3.760.2221410.18382802X-RAY DIFFRACTION100
3.76-40.23091450.16752758X-RAY DIFFRACTION100
4-4.310.18241460.14672806X-RAY DIFFRACTION100
4.31-4.740.17761130.13772811X-RAY DIFFRACTION100
4.74-5.420.17231510.14562776X-RAY DIFFRACTION100
5.42-6.830.20741560.15862804X-RAY DIFFRACTION100
6.83-49.880.16911910.15962801X-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