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Yorodumi- PDB-4e38: Crystal structure of probable keto-hydroxyglutarate-aldolase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+38 | ||||||
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Title | Crystal structure of probable keto-hydroxyglutarate-aldolase from Vibrionales bacterium SWAT-3 (Target EFI-502156) | ||||||
Components | Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase | ||||||
Keywords | LYASE / Structural Genomics | ||||||
Function / homology | Function and homology information 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity Similarity search - Function | ||||||
Biological species | Vibrionales bacterium SWAT-3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.64 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Allen, K.N. / Dunaway-Mariano, D. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of probable keto-hydroxyglutarate-aldolase from Vibrionales bacterium SWAT-3 (Target EFI-502156) Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Allen, K. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Allen, K.N. / Dunaway-Mariano, D. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e38.cif.gz | 145.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e38.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 4e38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/4e38 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/4e38 | HTTPS FTP |
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-Related structure data
Related structure data | 1vhcS S: Starting model for refinement |
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Similar structure data | |
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: 24766.326 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrionales bacterium SWAT-3 (bacteria) Gene: VSWAT3_13722 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5KUH7, 4-hydroxy-2-oxoglutarate aldolase #2: Chemical | ChemComp-CL / #3: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BIS-TRIS, 0.5M MAGNESIUM FORMATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→70 Å / Num. obs: 92852 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 8.1 % / Biso Wilson estimate: 28.894 Å2 / Rsym value: 0.053 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 2 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB entry 1VHC Resolution: 1.64→67.72 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.685 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.084 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.187 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→67.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.685 Å / Total num. of bins used: 20
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