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Yorodumi- PDB-3nxf: Robust computational design, optimization, and structural charact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nxf | ||||||
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Title | Robust computational design, optimization, and structural characterization of retroaldol enzymes | ||||||
Components | Retro-Aldolase | ||||||
Keywords | LYASE / computationally designed / retroaldolase / tim barrel | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | ||||||
Biological species | artificial gene (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Althoff, E.A. / Jiang, L. / Wang, L. / Lassila, J.K. / Moody, J. / Bolduc, J. / Wang, Z.Z. / Smith, M. / Hari, S. / Herschlag, D. ...Althoff, E.A. / Jiang, L. / Wang, L. / Lassila, J.K. / Moody, J. / Bolduc, J. / Wang, Z.Z. / Smith, M. / Hari, S. / Herschlag, D. / Stoddard, B.L. / Baker, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Authors: Wang, L. / Althoff, E.A. / Bolduc, J. / Jiang, L. / Moody, J. / Lassila, J.K. / Giger, L. / Hilvert, D. / Stoddard, B. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nxf.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nxf.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/3nxf ftp://data.pdbj.org/pub/pdb/validation_reports/nx/3nxf | HTTPS FTP |
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-Related structure data
Related structure data | 3o6yC 3ud6C 1a53S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29835.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) Description: THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS. Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein at 5mg/ml in 100mm NaCl, 25mm Tris pH 7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mm Na acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2009 / Details: Varimax HF | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.09→53.61 Å / Num. all: 11053 / Num. obs: 10320 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 46.1 Å2 / Net I/σ(I): 14.9 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A53, with design and adjacent residues pared to alanine Resolution: 2.4→53.61 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.814 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.58 / ESU R Free: 0.297 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.845 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→53.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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