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Yorodumi- PDB-4c6g: Structural Investigations into the Stereochemistry and Activity o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c6g | ||||||
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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 | ||||||
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: 2.1 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 | 4c6g.cif.gz | 475.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c6g.ent.gz | 391.2 KB | Display | PDB format |
PDBx/mmJSON format | 4c6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c6g_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 4c6g_full_validation.pdf.gz | 493.6 KB | Display | |
Data in XML | 4c6g_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 4c6g_validation.cif.gz | 112.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6g ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6g | HTTPS FTP |
-Related structure data
Related structure data | 4c5rC 4c5sC 4c5uC 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: 77546.641 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q68G84, EC: 5.4.3.-, phenylalanine ammonia-lyase #2: 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: 46.22 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.91 Å / Num. obs: 161887 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YII Resolution: 2.1→48.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.203 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.184 / 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: 46.036 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→48.73 Å
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Refine LS restraints |
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