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Yorodumi- PDB-3iae: Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iae | ||||||
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Title | Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate | ||||||
Components | Benzaldehyde lyase | ||||||
Keywords | LYASE / thiamine adduct | ||||||
Function / homology | Function and homology information acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / lyase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Brandt, G.S. / Petsko, G.A. / Ringe, D. / McLeish, M.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition. Authors: Brandt, G.S. / Kneen, M.M. / Petsko, G.A. / Ringe, D. / McLeish, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iae.cif.gz | 407.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iae.ent.gz | 337.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/3iae ftp://data.pdbj.org/pub/pdb/validation_reports/ia/3iae | HTTPS FTP |
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-Related structure data
Related structure data | 3iafC 3d7kS 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: 59894.055 Da / Num. of mol.: 2 / Mutation: A28S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Biovar I / Gene: bznB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F4L3, EC: 4.1.2.38 #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: 2.71 Å3/Da / Density % sol: 54.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM MES, 50% v/v PEG 200, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2006 / Details: Adjustable focusing mirrors in K-B geometry |
Radiation | Monochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 60682 / Num. obs: 60258 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.53 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D7K Resolution: 2.3→45.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.227 / 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: 48.093 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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