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Yorodumi- PDB-5lg5: Crystal structure of allantoin racemase from Pseudomonas fluoresc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lg5 | ||||||
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Title | Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR | ||||||
Components | Allantoin racemase | ||||||
Keywords | ISOMERASE / evolution of catalytic mechanisms / rate degradation / racemization intermediates / proton transfer / gene identification | ||||||
Function / homology | Function and homology information Isomerases; Racemases and epimerases; Acting on other compounds / allantoin racemase / allantoin racemase activity / racemase activity, acting on amino acids and derivatives / : Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cendron, l. / Zanotti, G. / Percudani, R. / Ragazzina, I. / Puggioni, V. / Maccacaro, E. / Liuzzi, A. / Secchi, A. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism. Authors: Cendron, L. / Ramazzina, I. / Puggioni, V. / Maccacaro, E. / Liuzzi, A. / Secchi, A. / 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 | 5lg5.cif.gz | 282.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lg5.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lg5 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lg5 | HTTPS FTP |
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-Related structure data
Related structure data | 5lfdC 5fldS 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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Unit cell |
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-Components
#1: Protein | Mass: 25842.611 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pGEM-AllR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E3SAZ9, allantoin racemase #2: 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: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M CaCl2, 0.1M HEPES pH 7.5, 28% w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97372 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97372 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.78 Å / Num. obs: 74201 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.3 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FLD Resolution: 2.1→39.78 Å / SU ML: 0.24 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.78 Å
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Refine LS restraints |
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LS refinement shell |
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