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- PDB-4d4f: Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d4f | ||||||
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Title | Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus | ||||||
![]() | CHALCONE ISOMERASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Kratzat, H. / Hinrichs, W. | ||||||
![]() | ![]() Title: Structural Basis for (2 R ,3 R )-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus. Authors: Palm, G.J. / Thomsen, M. / Berndt, L. / Hinrichs, W. #1: ![]() Title: Enzymatic Conversion of Flavonoids Using Bacterial Chalcone Isomerase and Enoate Reductase. Authors: Gall, M. / Thomsen, M. / Peters, C. / Pavlidis, I.V. / Jonczyk, P. / Grunert, P.P. / Beutel, S. / Scheper, T. / Gross, E. / Backes, M. / Geissler, T. / Ley, J.P. / Hilmer, J. / Krammer, G. / ...Authors: Gall, M. / Thomsen, M. / Peters, C. / Pavlidis, I.V. / Jonczyk, P. / Grunert, P.P. / Beutel, S. / Scheper, T. / Gross, E. / Backes, M. / Geissler, T. / Ley, J.P. / Hilmer, J. / Krammer, G. / Palm, G.J. / Hinrichs, W. / Bornscheuer, U.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 687.5 KB | Display | ![]() |
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PDB format | ![]() | 574.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8b7rC ![]() 8b7uC ![]() 8b7zC ![]() 4c9sS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | ![]() Mass: 32511.893 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / ![]() #3: Chemical | ChemComp-CL / ![]() #4: Water | ChemComp-HOH / | ![]() Sequence details | P250A MUTATION INTRODUCED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.64 Å3/Da / Density % sol: 73.5 % Description: THE RESIDUES 248-252 OF 4C9S WERE NOT INCLUDED IN THE TEMPLATE FOR MOLECULAR REPLACEMENT. |
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Crystal grow![]() | pH: 7.5 Details: 2.0 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5, 0.2 SODIUM CHLORIDE; CRYO: 2.4 M AMMONIUM SULPHATE, 22% GLYCEROL, 0.1 M HEPES PH 7.5, 0.2 SODIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.34→49.2 Å / Num. obs: 151554 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4C9S Resolution: 2.34→143.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.473 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 32.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→143.47 Å
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Refine LS restraints |
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