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- PDB-2uz1: 1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2uz1 | ||||||
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Title | 1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol | ||||||
![]() | (BENZALDEHYDE LYASE) x 2 | ||||||
![]() | LYASE / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / BENZOIN / FLAVOPROTEIN / BENZALDEHYDE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maraite, A. / Schmidt, T. / Ansorge-Schumacher, M.B. / Brzozowski, A.M. / Grogan, G. | ||||||
![]() | ![]() Title: Structure of the Thdp-Dependent Enzyme Benzaldehyde Lyase Refined to 1.65 A Resolution. Authors: Maraite, A. / Schmidt, T. / Ansorge-Schumacher, M.B. / Brzozowski, A.M. / Grogan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 444.3 KB | Display | ![]() |
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PDB format | ![]() | 360.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 92.7 KB | Display | |
Data in CIF | ![]() | 140 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ag0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58976.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 58976.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-TPP / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 37 % |
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Crystal grow | pH: 7.5 Details: 0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION ...Details: 0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION 5 MG ML-1 WITH A THREEFOLD STOICHIOMETRIC EXCESS OF THIAMINE DIPHOSPHATE (THDP). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 249612 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AG0 Resolution: 1.65→97.59 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.739 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / 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: 12.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→97.59 Å
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Refine LS restraints |
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