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Yorodumi- PDB-3czo: Crystal Structure of Double Mutant Phenylalanine Ammonia-Lyase Fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3czo | |||||||||
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Title | Crystal Structure of Double Mutant Phenylalanine Ammonia-Lyase From Anabaena Variabilis | |||||||||
Components | Histidine ammonia-lyase | |||||||||
Keywords | LYASE / Phenylalanine/histidine ammonia-lyase | |||||||||
Function / homology | Function and homology information phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylpropanoid biosynthetic process / phenylalanine ammonia-lyase activity / aromatic amino acid metabolic process / L-phenylalanine catabolic process / protein homotetramerization / cytoplasm Similarity search - Function | |||||||||
Biological species | Anabaena variabilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Stevens, R.C. / Wang, L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. Authors: Wang, L. / Gamez, A. / Archer, H. / Abola, E.E. / Sarkissian, C.N. / Fitzpatrick, P. / Wendt, D. / Zhang, Y. / Vellard, M. / Bliesath, J. / Bell, S.M. / Lemontt, J.F. / Scriver, C.R. / Stevens, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3czo.cif.gz | 420.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3czo.ent.gz | 346.5 KB | Display | PDB format |
PDBx/mmJSON format | 3czo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3czo_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 3czo_full_validation.pdf.gz | 500.7 KB | Display | |
Data in XML | 3czo_validation.xml.gz | 82.3 KB | Display | |
Data in CIF | 3czo_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3czo ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czo | HTTPS FTP |
-Related structure data
Related structure data | 2nynS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 59647.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q3M5Z3, histidine ammonia-lyase #2: Water | ChemComp-HOH / | Sequence details | RESIDUE MDO IS AUTOCATALY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12-20% PEG1500 and 100 mM SPG (succinic acid, sodium dihydrogen phosphate, glycine), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9183 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2007 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→134.8 Å / Num. all: 122951 / Num. obs: 122951 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2NYN Resolution: 2.2→34.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.845 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.276 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.548 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→34.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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