+Open data
-Basic information
Entry | Database: PDB / ID: 2yya | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GAR synthetase from Aquifex aeolicus | ||||||
Components | Phosphoribosylamine--glycine ligase | ||||||
Keywords | LIGASE / Glycinamide ribonucleotide synthetase / GAR synthetase / ATP binding / Purine nucleotide biosynthetic pathway / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Baba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biochem. / Year: 2010 Title: Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria Authors: Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yya.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yya.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 2yya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yya_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yya_full_validation.pdf.gz | 504.6 KB | Display | |
Data in XML | 2yya_validation.xml.gz | 39 KB | Display | |
Data in CIF | 2yya_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yya ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yya | HTTPS FTP |
-Related structure data
Related structure data | 2ip4C 2yrwC 2yrxC 2ys6C 2ys7C 2yw2SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47500.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) References: UniProt: O66949, phosphoribosylamine-glycine ligase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.10M succinic acid, 15%w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 3, 2006 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 33971 / % possible obs: 97.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.277 / % possible all: 92.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YW2 Resolution: 2.4→49.55 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 105493.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1679 Å2 / ksol: 0.364877 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|