[English] 日本語
Yorodumi- PDB-2h31: Crystal structure of human PAICS, a bifunctional carboxylase and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h31 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human PAICS, a bifunctional carboxylase and synthetase in purine biosynthesis | ||||||
Components | Multifunctional protein ADE2 | ||||||
Keywords | LIGASE / LYASE / alpha-beta-alpha | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process ...phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cadherin binding / extracellular exosome / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Li, S.-X. / Tong, Y.-P. / Xie, X.-C. / Li, S.-G. / Bi, R.-C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis. Authors: Li, S.X. / Tong, Y.P. / Xie, X.C. / Wang, Q.H. / Zhou, H.N. / Han, Y. / Zhang, Z.Y. / Gao, W. / Li, S.G. / Zhang, X.C. / Bi, R.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2h31.cif.gz | 84 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2h31.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 2h31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h31_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2h31_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 2h31_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 2h31_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/2h31 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/2h31 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 8||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a octamer generated from the monomer in the asymmetric unit by the operations: -x,-y,z and -y,x,z and y,-x,z and -x,y,-z and x,-y,-z and y,x,-z and -y,-x,-z. |
-Components
#1: Protein | Mass: 47463.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAICS, ADE2, AIRC, PAIS / Production host: Escherichia coli (E. coli) References: UniProt: P22234, phosphoribosylaminoimidazolesuccinocarboxamide synthase, phosphoribosylaminoimidazole carboxylase |
---|---|
#2: Chemical | ChemComp-CO2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0M succinic acid pH 7.0, 0.1M hepes pH 7.0, 0.5%(w/v) PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9780, 0.9796, 0.9643 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2005 | ||||||||||||
Radiation | Monochromator: SGM-TRAIN / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. all: 14136 / Num. obs: 14136 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| ||||||||||||||||||||
Refine LS restraints |
|