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- PDB-4v2r: Ironing out their differences: Dissecting the structural determin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v2r | |||||||||
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Title | Ironing out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase | |||||||||
![]() | PHENYLALANINE AMINOMUTASE (L-BETA-PHENYLALANINE FORMING) | |||||||||
![]() | LYASE | |||||||||
Function / homology | ![]() phenylalanine aminomutase (L-beta-phenylalanine forming) / intramolecular aminotransferase activity / paclitaxel biosynthetic process / phenylalanine ammonia-lyase / L-phenylalanine metabolic process / cinnamic acid biosynthetic process / alkaloid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / protein homotetramerization / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Heberling, M. / Masman, M. / Bartsch, S. / Wybenga, G.G. / Dijkstra, B.W. / Marrink, S. / Janssen, D. | |||||||||
![]() | ![]() Title: Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase. Authors: Heberling, M.M. / Masman, M.F. / Bartsch, S. / Wybenga, G.G. / Dijkstra, B.W. / Marrink, S.J. / Janssen, D.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.9 KB | Display | ![]() |
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PDB format | ![]() | 198.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v2qC ![]() 2yiiS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1236, 0.002039, 0.9923), Vector: |
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Components
#1: Protein | Mass: 77497.523 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q68G84, phenylalanine aminomutase (L-beta-phenylalanine forming), phenylalanine ammonia-lyase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.45 Å / Num. obs: 72574 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YII Resolution: 2.2→104.26 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.69 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.209 / 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: 29.125 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→104.26 Å
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Refine LS restraints |
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