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Yorodumi- PDB-4k29: Crystal structure of an enoyl-CoA hydratase/isomerase from Xantho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k29 | ||||||
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Title | Crystal structure of an enoyl-CoA hydratase/isomerase from Xanthobacter autotrophicus Py2 | ||||||
Components | Enoyl-CoA hydratase/isomerase | ||||||
Keywords | ISOMERASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / dimer of trimers / crotonase superfamily / oxyanion hole | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthobacter autotrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å | ||||||
Authors | Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of an enoyl-CoA hydratase/isomerase from Xanthobacter autotrophicus Py2 Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k29.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k29.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k29 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k29 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32567.848 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: Py2 / Gene: Xaut_3350 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A7IKN6 #2: Chemical | #3: Chemical | #4: 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: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.8M Potassium Sodium Tartrate, 0.1M TRIS, 0.5% PEGMME 5000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. all: 126795 / Num. obs: 126795 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.26 / Num. unique all: 6165 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.66→44.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.282 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.405 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→44.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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