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- PDB-3kum: Crystal structure of Dipeptide Epimerase from Enterococcus faecal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kum | ||||||
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Title | Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Arg-L-Tyr | ||||||
![]() | Dipeptide Epimerase | ||||||
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Function / homology | ![]() racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() 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 | ![]() | 532.5 KB | Display | ![]() |
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PDB format | ![]() | 440.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ijiC ![]() 3ijlC ![]() 3ijqC ![]() 3ik4C ![]() 3jvaSC ![]() 3jw7C ![]() 3jzuC ![]() 3k1gC ![]() 3q45C ![]() 3q4dC ![]() 3r0kC ![]() 3r0uC ![]() 3r10C ![]() 3r11C ![]() 3r1zC ![]() 3ritC ![]() 3ro6C 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37845.629 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ARG / ![]() #3: Chemical | ChemComp-TYR / ![]() #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→25 Å / Num. all: 245947 / Num. obs: 245947 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.081 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3JVA Resolution: 1.9→24.69 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2382726.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1701 Å2 / ksol: 0.367395 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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