+Open data
-Basic information
Entry | Database: PDB / ID: 3cl7 | ||||||
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Title | Crystal structure of Puue Allantoinase in complex with Hydantoin | ||||||
Components | Puue Allantoinase | ||||||
Keywords | HYDROLASE / Allantoinase / uric acid degradation / hydantoin | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ramazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases Authors: Ramazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cl7.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cl7.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3cl7 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3cl7 | HTTPS FTP |
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-Related structure data
Related structure data | 3cl6SC 3cl8C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35468.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pGEM-Puue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q3KFK7*PLUS, allantoinase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED ...THIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED IN UNIPROTKB LATER. | |
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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: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M (NH4)2SO4, 0.1M NaCacodylate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→53 Å / Num. all: 54454 / Num. obs: 54454 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / Num. unique all: 7551 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CL6 Resolution: 1.8→46.28 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.183 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.733 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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