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Yorodumi- PDB-4d4f: Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d4f | ||||||
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Title | Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus | ||||||
Components | CHALCONE ISOMERASE | ||||||
Keywords | ISOMERASE / FLAVONOIDS / NON-PROLYL CIS-PEPTIDE | ||||||
Function / homology | Chalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / Chalcone isomerase Function and homology information | ||||||
Biological species | EUBACTERIUM RAMULUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Thomsen, M. / Kratzat, H. / Hinrichs, W. | ||||||
Citation | Journal: Molecules / Year: 2022 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: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d4f.cif.gz | 687.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d4f.ent.gz | 574.6 KB | Display | PDB format |
PDBx/mmJSON format | 4d4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/4d4f ftp://data.pdbj.org/pub/pdb/validation_reports/d4/4d4f | 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 (ref.) |
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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 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.) EUBACTERIUM RAMULUS (bacteria) / Description: DSM 16296 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: V9P0A9, chalcone isomerase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
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: 0.918 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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