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Yorodumi- PDB-3q4d: Crystal structure of dipeptide epimerase from Cytophaga hutchinso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q4d | ||||||
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Title | Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala | ||||||
Components | Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase | ||||||
Keywords | ISOMERASE / (beta/alpha)8-barrel | ||||||
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 / magnesium ion binding Similarity search - Function | ||||||
Biological species | Cytophaga hutchinsonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lukk, T. / Gerlt, J.A. / Nair, S.K. | ||||||
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 | 3q4d.cif.gz | 622.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q4d.ent.gz | 515 KB | Display | PDB format |
PDBx/mmJSON format | 3q4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/3q4d ftp://data.pdbj.org/pub/pdb/validation_reports/q4/3q4d | HTTPS FTP |
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-Related structure data
Related structure data | 3ijiC 3ijlC 3ijqC 3ik4C 3jvaC 3jw7C 3jzuC 3k1gC 3kumC 3q45C 3r0kC 3r0uC 3r10C 3r11C 3r1zC 3ritC 3ro6C 1tkkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 40353.527 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU2140, CHU_2140, tfdD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q11T61, chloromuconate cycloisomerase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DAL / #4: Chemical | ChemComp-ALA / #5: 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: 3.69 Å3/Da / Density % sol: 66.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, Protein concentration was 40 mg/mL, pH 4.0, VAPOR ...Details: Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→20 Å / Num. obs: 105392 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TKK Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / 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: 66.3 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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