[English] 日本語
Yorodumi- PDB-1pwh: Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwh | ||||||
---|---|---|---|---|---|---|---|
Title | Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE | ||||||
Components | L-serine dehydratase | ||||||
Keywords | LYASE / Rat Liver / L-Serine Dehydratase / Complex | ||||||
Function / homology | Function and homology information Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / threonine catabolic process / L-serine ammonia-lyase / L-serine ammonia-lyase activity / pyruvate biosynthetic process / L-serine catabolic process / isoleucine biosynthetic process / response to cobalamin ...Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / threonine catabolic process / L-serine ammonia-lyase / L-serine ammonia-lyase activity / pyruvate biosynthetic process / L-serine catabolic process / isoleucine biosynthetic process / response to cobalamin / response to amino acid / response to nutrient levels / gluconeogenesis / lipid metabolic process / pyridoxal phosphate binding / protein-containing complex assembly / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yamada, T. / Komoto, J. / Takata, Y. / Ogawa, H. / Takusagawa, F. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal structure of serine dehydratase from rat liver. Authors: Yamada, T. / Komoto, J. / Takata, Y. / Ogawa, H. / Pitot, H.C. / Takusagawa, F. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT CHAINS AB, CD FORM HOMODIMERS IN TERMS OF STRUCTURE. HOWEVER, SINCE THE ACTIVE SITE IN ONE SUBUNIT IS INDEPENDENT FROM THE OTHER SUBUNIT, THE ENZYMATIC REACTION PROCEEDS MONOMERICALLY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pwh.cif.gz | 247.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pwh.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwh ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwh | HTTPS FTP |
---|
-Related structure data
Related structure data | 1pweSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34506.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCWOri+ / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P09367, L-serine ammonia-lyase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PLV / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, potassium Acetate, TrisHCL, Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 22K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 5, 2003 / Details: mirrors |
Radiation | Monochromator: GRAPHITE + MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 40706 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 1692.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 491.7 / Num. unique all: 3051 / Rsym value: 0.28 / % possible all: 75.4 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 40796 / Num. measured all: 271545 |
Reflection shell | *PLUS Rmerge(I) obs: 0.124 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Apo Enzyme 1PWE Resolution: 2.6→25.01 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.7014 Å2 / ksol: 0.33981 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25.01 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor Rwork: 0.3 |