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- PDB-6z92: [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) solved... -

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Basic information

Entry
Database: PDB / ID: 6z92
Title[4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) solved by Fe-SAD phasing
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 / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / DUF523 domain-containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.067 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
DepositionJun 3, 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,28210
Polymers35,1622
Non-polymers1,1208
Water2,216123
1
A: DUF523 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0574
Polymers17,5811
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF523 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2256
Polymers17,5811
Non-polymers6445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.28, 85.911, 39.565
Angle α, β, γ (deg.)90, 93.64, 90
Int Tables number5
Space group name H-MC121

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Components

#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
#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystallization in 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: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.07→66.51 Å / Num. obs: 18594 / % possible obs: 89.8 % / Redundancy: 4.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.161 / Net I/σ(I): 7.6
Reflection shellResolution: 2.07→2.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4189 / CC1/2: 0.31 / Rrim(I) all: 1.421 / % possible all: 41.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMar 15, 2019 (BUILT 20190315)data reduction
STARANISO2.2.15data scaling
autoSHARPautoSHARP_2018phasing
RefinementMethod to determine structure: SAD / Resolution: 2.067→66.51 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.234 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 888 -RANDOM
Rwork0.1948 ---
obs0.196 18594 68.1 %-
Displacement parametersBiso mean: 38.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.6986 Å20 Å2-0.2101 Å2
2---2.656 Å20 Å2
3---0.9574 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.067→66.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 43 123 2376
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082300HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.923114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d788SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes391HARMONIC5
X-RAY DIFFRACTIONt_it2300HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2018SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion15.92
LS refinement shellResolution: 2.07→2.22 Å
RfactorNum. reflection% reflection
Rfree0.1683 23 -
Rwork0.2177 --
obs0.2148 423 8.06 %

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