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Yorodumi- PDB-4kpk: Crystal structure of a enoyl-CoA hydratase from Shewanella pealea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kpk | ||||||
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Title | Crystal structure of a enoyl-CoA hydratase from Shewanella pealeana ATCC 700345 | ||||||
Components | Enoyl-CoA hydratase/isomerase | ||||||
Keywords | ISOMERASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / enoyl-CoA hydratase | ||||||
Function / homology | Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / isomerase activity / Alpha-Beta Complex / Alpha Beta / Enoyl-CoA hydratase/isomerase Function and homology information | ||||||
Biological species | Shewanella pealeana (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å | ||||||
Authors | Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / 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 a enoyl-CoA hydratase from Shewanella pealeana ATCC 700345 Authors: Kumaran, D. / 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 | 4kpk.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kpk.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/4kpk ftp://data.pdbj.org/pub/pdb/validation_reports/kp/4kpk | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35435.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella pealeana (bacteria) / Strain: ATCC 700345 / Gene: Spea_2799 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: A8H6D2 |
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#2: Chemical | ChemComp-EDO / |
#3: 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: 1.89 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate, 0.1M Tris 25% PEG 4000 and 5% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2013 / Details: mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 14646 / Num. obs: 14646 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1119 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→36.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.4 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.194 / 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: 32.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→36.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 Å / Total num. of bins used: 20
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