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- PDB-5lfd: Crystal structure of allantoin racemase from Pseudomonas fluoresc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lfd | ||||||
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Title | Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR | ||||||
![]() | Allantoin racemase | ||||||
![]() | ISOMERASE / evolution of catalytic mechanisms / rate degradation / racemization intermediates / proton transfer / gene identification | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cendron, l. / Zanotti, G. / Percudani, R. / Ramazzina, I. / Puggioni, V. / Maccacaro, E. / Liuzzi, A. / Secchi, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lg5C ![]() 2eq5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 1 - 234 / Label seq-ID: 1 - 234
NCS oper:
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Components
#1: Protein | Mass: 25842.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 8% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→77.58 Å / Num. obs: 24255 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 12.1 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2EQ5 Resolution: 2.15→44.83 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 7.384 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 23.198 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→44.83 Å
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Refine LS restraints |
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