[English] 日本語
Yorodumi- PDB-1t6p: Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides | |||||||||
Components | phenylalanine ammonia-lyase | |||||||||
Keywords | LYASE / triple helix coiled coil / MIO / cinnamate | |||||||||
Function / homology | Function and homology information phenylalanine/tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Rhodosporidium toruloides (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Calabrese, J.C. / Jordan, D.B. | |||||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Authors: Calabrese, J.C. / Jordan, D.B. / Boodhoo, A. / Sariaslani, S. / Vannelli, T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t6p.cif.gz | 964.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t6p.ent.gz | 808.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t6p_validation.pdf.gz | 559.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1t6p_full_validation.pdf.gz | 718.9 KB | Display | |
Data in XML | 1t6p_validation.xml.gz | 193.1 KB | Display | |
Data in CIF | 1t6p_validation.cif.gz | 258.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6p ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6p | HTTPS FTP |
-Related structure data
Related structure data | 1t6jSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 77655.930 Da / Num. of mol.: 8 / Fragment: ammonia lyase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodosporidium toruloides (fungus) / Gene: PAL / Plasmid: pET-24a pEAL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: P11544, EC: 4.3.1.5 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3000, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 78 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.980647 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2000 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980647 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25.1 Å / Num. all: 146898 / Num. obs: 146898 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 3.17 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.14 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.87 / % possible all: 80.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1T6J Resolution: 2.7→25.1 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→25.1 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|