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Yorodumi- PDB-6xjm: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xjm | |||||||||
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Title | Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret | |||||||||
Components | Biuret hydrolase | |||||||||
Keywords | HYDROLASE / TrtA / BiuH / triuret / biuret / cysteine hydrolase / nitrogen | |||||||||
Function / homology | Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / dicarbonimidic diamide / Biuret hydrolase Function and homology information | |||||||||
Biological species | Rhodococcus sp. Mel (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Tassoulas, L.T. / Elias, M.H. / Wackett, L.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway. Authors: Tassoulas, L.J. / Elias, M.H. / Wackett, L.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xjm.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xjm.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xjm ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xjm | HTTPS FTP |
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-Related structure data
Related structure data | 6xixC 6xj4C 6xjeC 6xk1C 6azoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26044.336 Da / Num. of mol.: 4 / Mutation: C169S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. Mel (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8ZKV9 #2: Chemical | ChemComp-C5J / #3: Water | ChemComp-HOH / | 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: 2.03 Å3/Da / Density % sol: 39.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1uL 5 mg/mL protein + 1uL 20% w/v PEG3350, 0.2M MgCl2, 20mM Biuret pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99184 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→81.8 Å / Num. obs: 102760 / % possible obs: 99.7 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.42 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 4.32 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 13718 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6AZO Resolution: 2.05→56.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.695 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.179 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.7 Å2 / Biso mean: 21.2 Å2 / Biso min: 11.6 Å2
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Refinement step | Cycle: final / Resolution: 2.05→56.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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