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

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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 / 4 iron, 4 sulfur cluster binding / metal ion binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-SF4 / 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


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


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


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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 %

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