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- PDB-3der: Crystal structure of dipeptide epimerase from Thermotoga maritima... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3der | ||||||
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Title | Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Lys dipeptide | ||||||
![]() | Muconate cycloisomerase | ||||||
![]() | ISOMERASE / dipeptide epimerase / Thermotoga maritima / enzymatic function | ||||||
Function / homology | ![]() L-Ala-D/L-Glu epimerase activity / L-Ala-D/L-Glu epimerase / racemase and epimerase activity, acting on amino acids and derivatives / cell wall organization / cell wall macromolecule catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() Title: Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Authors: Kalyanaraman, C. / Imker, H.J. / Fedorov, A.A. / Fedorov, E.V. / Glasner, M.E. / 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 | ![]() | 284.6 KB | Display | ![]() |
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PDB format | ![]() | 231.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3deqSC ![]() 3desC ![]() 3dfyC 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38717.285 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ALA / #4: Chemical | ChemComp-LYS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 3.0 M Sodium chloride, 0.1 M Sodium acetate trihydrate, pH 4.5, 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: Sep 15, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 230926 / Num. obs: 230926 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.084 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3DEQ Resolution: 1.9→24.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2919185.13 / 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: 41.7652 Å2 / ksol: 0.374441 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
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Xplor file |
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