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Yorodumi- PDB-4k2n: Crystal structure of an enoyl-CoA hydratase/ carnithine racemase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k2n | ||||||
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Title | Crystal structure of an enoyl-CoA hydratase/ carnithine racemase from Magnetospirillum magneticum | ||||||
Components | Enoyl-CoA hydratase/carnithine racemase | ||||||
Keywords | ISOMERASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / crotonase-like / oxyanion hole | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Magnetospirillum magneticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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/ carnithine racemase from Magnetospirillum magneticum 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 | 4k2n.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k2n.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k2n_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 4k2n_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | 4k2n_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4k2n_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k2n ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k2n | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 30975.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum magneticum (bacteria) / Strain: AMB-1 / Gene: amb1315 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2W7Q6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium Chloride, HEPES, PEG3350, pH 7.5, 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: 2→50 Å / Num. all: 19654 / Num. obs: 19654 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 33.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 33.6 % / Rmerge(I) obs: 0.667 / Num. unique all: 1927 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→42.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.969 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.144 / 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: 35.562 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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