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- PDB-3q45: Crystal structure of Dipeptide Epimerase from Cytophaga hutchinso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q45 | ||||||
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Title | Crystal structure of Dipeptide Epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Val | ||||||
![]() | Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase | ||||||
![]() | ISOMERASE / (beta/alpha)8-barrel | ||||||
Function / homology | ![]() racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukk, T. / Gerlt, J.A. / Nair, S.K. | ||||||
![]() | ![]() Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 622.7 KB | Display | ![]() |
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PDB format | ![]() | 515.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 533.4 KB | Display | ![]() |
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Full document | ![]() | 596.5 KB | Display | |
Data in XML | ![]() | 115.5 KB | Display | |
Data in CIF | ![]() | 149.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ijiC ![]() 3ijlC ![]() 3ijqC ![]() 3ik4C ![]() 3jvaC ![]() 3jw7C ![]() 3jzuC ![]() 3k1gC ![]() 3kumC ![]() 3q4dC ![]() 3r0kC ![]() 3r0uC ![]() 3r10C ![]() 3r11C ![]() 3r1zC ![]() 3ritC ![]() 3ro6C ![]() 1tkkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
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Components
#1: Protein | Mass: 40353.527 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DAL / #4: Chemical | ChemComp-VAL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Precipitant contained 12% PEG 10000 and 0.1M Na-citrate, Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Val. Protein concentration was 40 mg/mL, pH 4.0, VAPOR ...Details: Precipitant contained 12% PEG 10000 and 0.1M Na-citrate, Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Val. Protein concentration was 40 mg/mL, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 4, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→20 Å / Num. obs: 104809 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.53 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TKK Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.323 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.076 Å / Total num. of bins used: 20
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