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Yorodumi- PDB-2nyf: Crystal structure of phenylalanine ammonia-lyase from Nostoc punc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nyf | |||||||||
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Title | Crystal structure of phenylalanine ammonia-lyase from Nostoc punctiforme | |||||||||
Components | Nostoc punctiforme phenylalanine ammonia lyase | |||||||||
Keywords | LYASE / Methylidene imidazolone prosthetic group (autocatalytically formed by internal tripeptide segment Ala167-Ser168-Gly169) | |||||||||
Function / homology | Function and homology information phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / phenylpropanoid biosynthetic process / aromatic amino acid metabolic process / protein homotetramerization / cytoplasm Similarity search - Function | |||||||||
Biological species | Nostoc punctiforme (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Louie, G.V. / Moffitt, M.C. / Bowman, M.E. / Pence, J. / Noel, J.P. / Moore, B.S. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Discovery of Two Cyanobacterial Phenylalanine Ammonia Lyases: Kinetic and Structural Characterization. Authors: Moffitt, M.C. / Louie, G.V. / Bowman, M.E. / Pence, J. / Noel, J.P. / Moore, B.S. | |||||||||
History |
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Remark 600 | HETEROGEN Residue MDO is autocatalytically formed by internal tripeptide segment Ala167-Ser168-Gly169 | |||||||||
Remark 999 | Sequence No suitable database references were found at time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nyf.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nyf.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 2nyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/2nyf ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nyf | HTTPS FTP |
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-Related 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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Details | The 222 symmetric homotetramer is generated by crystallographic symmetry. |
-Components
#1: Protein | Mass: 62264.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: B2J528*PLUS, histidine ammonia-lyase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M MOPSO (pH 7.0), 21% (w/v) polyethylene glycol 8000, 0.2 M lithium sulfate, 2 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 18191 / Num. obs: 16902 / % possible obs: 92.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.56 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1809 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / Isotropic thermal model: Isotropic / Cross valid method: Random / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.1 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å /
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