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Yorodumi- PDB-3jw7: Crystal structure of Dipeptide Epimerase from Enterococcus faecal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jw7 | ||||||
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Title | Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Ile-L-Tyr | ||||||
Components | Dipeptide Epimerase | ||||||
Keywords | ISOMERASE / Dipeptide Epimerase / enolase superfamily / dipeptide L-Ile-L-Tyr | ||||||
Function / homology | Function and homology information 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 / amino acid catabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis V583 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Sakai, A. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jw7.cif.gz | 555.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jw7.ent.gz | 454 KB | Display | PDB format |
PDBx/mmJSON format | 3jw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jw7 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jw7 | HTTPS FTP |
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-Related structure data
Related structure data | 3ijiC 3ijlC 3ijqC 3ik4C 3jvaSC 3jzuC 3k1gC 3kumC 3q45C 3q4dC 3r0kC 3r0uC 3r10C 3r11C 3r1zC 3ritC 3ro6C 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 37845.629 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Gene: EF_1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834W6 |
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-Non-polymers , 5 types, 1657 molecules
#2: Chemical | ChemComp-ILE / #3: Chemical | ChemComp-TYR / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / #6: 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: 2.77 Å3/Da / Density % sol: 55.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4M Sodium Citrate, 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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2008 |
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: 1.8→25 Å / Num. all: 299981 / Num. obs: 299981 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.085 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JVA Resolution: 1.8→25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1603533.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.14 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4839 Å2 / ksol: 0.371558 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
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Xplor file |
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