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- PDB-2ys6: Crystal structure of GAR synthetase from Geobacillus kaustophilus -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ys6 | ||||||
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Title | Crystal structure of GAR synthetase from Geobacillus kaustophilus | ||||||
![]() | Phosphoribosylglycinamide synthetase | ||||||
![]() | 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 | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.6 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.9 KB | Display | ![]() |
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Full document | ![]() | 806 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ip4C ![]() 2yrwSC ![]() 2yrxC ![]() 2ys7C ![]() 2yw2C ![]() 2yyaC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 48228.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5L3C7, phosphoribosylamine-glycine ligase |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-AMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M sodium dihydrogen phosphate monohydrate, 20%w/v polyethylene glycol 3350, 10mM ATP, 10mM Gly, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 15, 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: 2.2→50 Å / Num. obs: 21104 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.424 / Num. unique all: 2041 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YRW Resolution: 2.21→38.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72267.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.5589 Å2 / ksol: 0.37007 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→38.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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