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Yorodumi- PDB-4ja0: Crystal structure of the invertebrate bi-functional purine biosyn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ja0 | ||||||
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Title | Crystal structure of the invertebrate bi-functional purine biosynthesis enzyme PAICS at 2.8 A resolution | ||||||
Components | Phosphoribosylaminoimidazole carboxylase | ||||||
Keywords | PROTEIN BINDING / SAICAR PurE / Purine biosynthesis | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / 'de novo' IMP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Taschner, M. / Basquin, J. / Benda, C. / Lorentzen, E. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 angstrom resolution. Authors: Taschner, M. / Basquin, J. / Benda, C. / Lorentzen, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ja0.cif.gz | 304 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ja0.ent.gz | 245.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ja0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ja0_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 4ja0_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 4ja0_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 4ja0_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4ja0 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4ja0 | HTTPS FTP |
-Related structure data
Related structure data | 2h31S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47407.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: Q1HQ66 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50mM Tris, 2M Ammonium sulfate, 1% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 46866 / Num. obs: 46715 / % possible obs: 0.997 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.525 / % possible all: 97.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H31 Resolution: 2.8→46.711 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.711 Å
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Refine LS restraints |
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LS refinement shell |
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