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Yorodumi- PDB-4bvs: Cyanuric acid hydrolase: evolutionary innovation by structural co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bvs | |||||||||
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Title | Cyanuric acid hydrolase: evolutionary innovation by structural concatenation. | |||||||||
Components | CYANURIC ACID AMIDOHYDROLASE | |||||||||
Keywords | HYDROLASE / AMIDASE | |||||||||
Function / homology | Function and homology information cyanuric acid amidohydrolase / cyanuric acid amidohydrolase activity / atrazine catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS SP. ADP (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Peat, T.S. / Balotra, S. / Wilding, M. / French, N.G. / Briggs, L.J. / Panjikar, S. / Cowieson, N. / Newman, J. / Scott, C. | |||||||||
Citation | Journal: Mol.Microbiol. / Year: 2013 Title: Cyanuric Acid Hydrolase: Evolutionary Innovation by Structural Concatenation. Authors: Peat, T.S. / Balotra, S. / Wilding, M. / French, N.G. / Briggs, L.J. / Panjikar, S. / Cowieson, N. / 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 | 4bvs.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bvs.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bvs_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 4bvs_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 4bvs_validation.xml.gz | 26 KB | Display | |
Data in CIF | 4bvs_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvs ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvs | HTTPS FTP |
-Related structure data
Related structure data | 4bvqC 4bvrC 4bvtC 3zgr 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 363 / Label seq-ID: 20 - 383
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-Components
#1: Protein | Mass: 40418.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) Description: GENE SYNTHESIZED BASED ON SEQUENCE FROM ACCESSION NO U66917 Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P58329, cyanuric acid amidohydrolase #2: Chemical | #3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: THE PROTEIN WAS DIALYSED AGAINST HEPES BUFFER WITH MELAMINE AND THE FINAL CONCENTRATION OF PROTEIN WAS 2 MG/ML. THIS COMPLEX WAS SET UP IN A 3:2 RATIO WITH 147 MM NACL, 32% V/V PEG 400 AND 100 MM HEPES PH 7.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→42.2 Å / Num. obs: 22546 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZGR 3zgr Resolution: 2.6→42.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.529 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→42.29 Å
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Refine LS restraints |
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