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Yorodumi- PDB-2o7f: Tyrosine ammonia-lyase from Rhodobacter sphaeroides (His89Phe var... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o7f | |||||||||
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Title | Tyrosine ammonia-lyase from Rhodobacter sphaeroides (His89Phe variant), complexed with coumaric acid | |||||||||
Components | Putative histidine ammonia-lyase | |||||||||
Keywords | LYASE / Methylidene imidazolone prosthetic group | |||||||||
Function / homology | Function and homology information tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / phenylpropanoid biosynthetic process / phenylalanine ammonia-lyase activity / tyrosine catabolic process / protein homotetramerization / identical protein binding Similarity search - Function | |||||||||
Biological species | Rhodobacter sphaeroides (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Louie, G.V. / Bowman, M.E. / Moffitt, M.C. / Baiga, T.J. / Moore, B.S. / Noel, J.P. | |||||||||
Citation | Journal: Chem.Biol. / Year: 2006 Title: Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Authors: Louie, G.V. / Bowman, M.E. / Moffitt, M.C. / Baiga, T.J. / Moore, B.S. / Noel, J.P. | |||||||||
History |
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Remark 999 | Sequence Residue MDO is autocatalytically formed by internal tripeptide segment Ala149-Ser150-Gly151 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o7f.cif.gz | 811.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o7f.ent.gz | 664.8 KB | Display | PDB format |
PDBx/mmJSON format | 2o7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o7f_validation.pdf.gz | 514.8 KB | Display | wwPDB validaton report |
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Full document | 2o7f_full_validation.pdf.gz | 555.6 KB | Display | |
Data in XML | 2o7f_validation.xml.gz | 170 KB | Display | |
Data in CIF | 2o7f_validation.cif.gz | 244.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/2o7f ftp://data.pdbj.org/pub/pdb/validation_reports/o7/2o7f | HTTPS FTP |
-Related structure data
Related structure data | 2o6ySC 2o78C 2o7bC 2o7dC 2o7eC 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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2 |
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Unit cell |
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Details | The 222-symmetric homotetramer includes chains A, B, C, and D. / The 222-symmetric homotetramer includes chains E, F, G, and H. |
-Components
#1: Protein | Mass: 54954.715 Da / Num. of mol.: 8 / Mutation: H89F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: hutH / Plasmid: pHis8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3IWB0, EC: 4.3.1.- #2: Chemical | ChemComp-HC4 / #3: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M MOPSO (pH 7.0), 7% (w/v) polyethylene glycol 8000, 0.3 M ammonium acetate, 2 mM dithiothreitol, 35 mM cyclohexylbutanoyl-N-hydroxyethylglucamide, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2006 |
Radiation | Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2→500 Å / Num. obs: 282535 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2o6y (tyrosine ammonia-lyase from Rhodobacter sphaeroides) Resolution: 2→500 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: 16.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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