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Yorodumi- PDB-4c5r: Structural Investigations into the Stereochemistry and Activity o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c5r | |||||||||
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Title | Structural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus chinensis | |||||||||
Components | PHENYLALANINE AMMONIA-LYASE | |||||||||
Keywords | LYASE / (R)-BETA-PHENYLALANINE ANALOGUE | |||||||||
Function / homology | Function and homology information 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 | TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | |||||||||
Authors | Wybenga, G.G. / Szymanski, W. / Wu, B. / Feringa, B.L. / Janssen, D.B. / Dijkstra, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural Investigations Into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus Chinensis. Authors: Wybenga, G.G. / Szymanski, W. / Wu, B. / Feringa, B.L. / Janssen, D.B. / Dijkstra, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c5r.cif.gz | 496.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c5r.ent.gz | 407.4 KB | Display | PDB format |
PDBx/mmJSON format | 4c5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c5r_validation.pdf.gz | 505.3 KB | Display | wwPDB validaton report |
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Full document | 4c5r_full_validation.pdf.gz | 531.9 KB | Display | |
Data in XML | 4c5r_validation.xml.gz | 91.1 KB | Display | |
Data in CIF | 4c5r_validation.cif.gz | 126.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5r ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5r | HTTPS FTP |
-Related structure data
Related structure data | 4c5sC 4c5uC 4c6gC 4cq5C 2yiiS 4c5t 4c5v C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 77553.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PEPTIDE BOND BETWEEN SER174 AND MDO 175 PEPTIDE BOND BETWEEN MDO 175 AND D178 COVALENT BOND BETWEEN THE CB2 ATOM OF MDO AND THE BETA-AMINO GROUP OF THE R-BETA-PHE SUBSTRATE ANALOGUE Source: (gene. exp.) TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q68G84, phenylalanine ammonia-lyase #2: Chemical | ChemComp-BQ7 / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→49.09 Å / Num. obs: 151434 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.14→2.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YII Resolution: 2.14→49.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.497 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.173 / 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: 25.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→49.09 Å
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Refine LS restraints |
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