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Yorodumi- PDB-6azo: Structural and biochemical characterization of a non-canonical bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6azo | ||||||
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Title | Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841 | ||||||
Components | Putative amidase | ||||||
Keywords | HYDROLASE / s-triazine / xenobiotic | ||||||
Function / homology | biuret amidohydrolase / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / Biuret amidohydrolase Function and homology information | ||||||
Biological species | Rhizobium leguminosarum bv. viciae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å | ||||||
Authors | Peat, T.S. / Esquirol, L. / Newman, J. / Scott, C. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. Authors: Esquirol, L. / Peat, T.S. / Wilding, M. / Lucent, D. / French, N.G. / Hartley, C.J. / Newman, J. / Scott, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6azo.cif.gz | 190.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6azo.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 6azo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6azo_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 6azo_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 6azo_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 6azo_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6azo ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 29072.729 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium leguminosarum bv. viciae (strain 3841) (bacteria) Strain: 3841 / Gene: pRL100352 / Plasmid: pETcc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q1M7F4 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.96 Å3/Da / Density % sol: 37.23 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: Protein at 4 mg/mL was set up in 200 nL plus 200 nL drops with reservoir: 100 mM bis-tris chloride at pH 6.1, 20.7% (w/v) PEG 4000, 89 mM lithium sulfate at 8C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→47.9 Å / Num. obs: 32094 / % possible obs: 99.7 % / Redundancy: 19.8 % / CC1/2: 0.991 / Rpim(I) all: 0.066 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3560 / CC1/2: 0.817 / Rpim(I) all: 0.307 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.46→44.99 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.83 / SU B: 12.347 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 1.997 / ESU R Free: 0.342 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.304 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→44.99 Å
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Refine LS restraints |
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