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Yorodumi- PDB-6z96: [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z96 | ||||||
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Title | [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked with 4-thiouracil (12.65 keV, 7.125 keV (Fe-SAD) and 6.5 keV (S-SAD) data) | ||||||
Components | TudS | ||||||
Keywords | TRANSFERASE / thiouracil / iron-sulfur cluster / desulfuration / sulfurtransferase | ||||||
Function / homology | 2-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 species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.327 Å | ||||||
Authors | Pecqueur, L. / Zhou, J. / Fontecave, M. / Golinelli-Pimpaneau, B. | ||||||
Funding support | France, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z96.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z96.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 6z96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z96_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6z96_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6z96_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6z96_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/6z96 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/6z96 | HTTPS FTP |
-Related structure data
Related structure data | 6z92SC 6z93C 6z94C 6zw9C 6z95 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17580.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4Z949 |
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-Non-polymers , 5 types, 342 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Anaeroby, 10 mM MgCl2, 0.1 M MES, pH 5.5, 7-9% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→39.69 Å / Num. obs: 69773 / % possible obs: 92.2 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.33→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 1.151 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3489 / CC1/2: 0.548 / Rrim(I) all: 1.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z92 Resolution: 1.327→39.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.055
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Displacement parameters | Biso mean: 25.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.327→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.44 Å
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