[English] 日本語
Yorodumi
- PDB-6zw9: [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zw9
Title[4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked with 4-thiouracil (S-SAD data)
ComponentsDUF523 domain-containing protein
KeywordsTRANSFERASE / thiouracil / iron-sulfur cluster / desulfuration / sulfurtransferase
Function / homology2-thiouracil desulfurase / 2-thiouracil desulfurase / HYDROSULFURIC ACID / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / DUF523 domain-containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å
AuthorsPecqueur, L. / Zhou, J. / Fontecave, M. / Golinelli-Pimpaneau, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyLABEX DYNAMO, ANR-11-LABX-0011-01 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Evidence for a [4Fe-5S] Intermediate in the Non-Redox Desulfuration of Thiouracil.
Authors: Zhou, J. / Pecqueur, L. / Aucynaite, A. / Fuchs, J. / Rutkiene, R. / Vaitekunas, J. / Meskys, R. / Boll, M. / Fontecave, M. / Urbonavicius, J. / Golinelli-Pimpaneau, B.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF523 domain-containing protein
B: DUF523 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1649
Polymers35,1622
Non-polymers1,0027
Water7,422412
1
A: DUF523 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1355
Polymers17,5811
Non-polymers5544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF523 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0294
Polymers17,5811
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.165, 85.519, 39.576
Angle α, β, γ (deg.)90, 94.01, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-492-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DUF523 domain-containing protein


Mass: 17580.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4Z949

-
Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: Anaeroby, 10 mM MgCl2, 0.1 M MES, pH 5.5, 7-9% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.90745 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.90745 Å / Relative weight: 1
ReflectionResolution: 1.759→42.76 Å / Num. obs: 39587 / % possible obs: 91.2 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.086 / Net I/σ(I): 18.9
Reflection shellResolution: 1.76→1.84 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.253 / Num. unique obs: 1978 / CC1/2: 0.955 / Rrim(I) all: 0.283 / % possible all: 40.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMar 15,2019 (BUILT 20190806)data reduction
STARANISO2.2.19data scaling
BUSTER2.10.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z92

6z92


Resolution: 1.759→24.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 1967 -RANDOM
Rwork0.1679 ---
obs0.1689 39569 88.1 %-
Displacement parametersBiso mean: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.2058 Å20 Å2-0.0888 Å2
2--0.3112 Å20 Å2
3----0.1054 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.759→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 33 412 2671
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082382HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913245HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d824SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes415HARMONIC5
X-RAY DIFFRACTIONt_it2382HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2728SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion13.05
LS refinement shellResolution: 1.76→1.8 Å
RfactorNum. reflection% reflection
Rfree0.2925 36 -
Rwork0.3599 --
obs0.3566 792 23.85 %

+
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