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- PDB-4pzf: Berberine bridge enzyme G164A variant, a reticuline dehydrogenase -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pzf | |||||||||
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Title | Berberine bridge enzyme G164A variant, a reticuline dehydrogenase | |||||||||
![]() | Reticuline oxidase | |||||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / BI-COVALENT FLAVINYLATION / Reticuline oxidase / Berberine bridge-forming enzyme / Tetrahydroprotoberberine synthase | |||||||||
Function / homology | ![]() reticuline oxidase / reticuline oxidase activity / alkaloid metabolic process / FAD binding / cytoplasmic vesicle Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zafred, D. / Wallner, S. / Steiner, B. / Macheroux, P. | |||||||||
![]() | ![]() Title: Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. Authors: Zafred, D. / Steiner, B. / Teufelberger, A.R. / Hromic, A. / Karplus, P.A. / Schofield, C.J. / Wallner, S. / Macheroux, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 412.8 KB | Display | ![]() |
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PDB format | ![]() | 337.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 73.4 KB | Display | |
Data in CIF | ![]() | 97.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pveC ![]() 4pvhC ![]() 4pvjC ![]() 4pvkC ![]() 4pwbC ![]() 4pwcC ![]() 3d2hS C: citing same article ( 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60061.008 Da / Num. of mol.: 4 / Mutation: G164A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BBE1 / Production host: ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 319 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/12P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/12P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | CONFLICT MUTATIONS ARE CLEAVING SITES. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30mg/mL protein + 0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate, BATCH, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2014 |
Radiation | Monochromator: carved single silicon (111) crystal with a channel in the middle (called channel-cut design) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 141762 / Num. obs: 140296 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Net I/σ(I): 11.78 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.63 / Num. unique all: 17490 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3D2H Resolution: 2.2→47.378 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.378 Å
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Refine LS restraints |
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LS refinement shell |
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