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Open data
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Basic information
Entry | Database: PDB / ID: 1gso | ||||||
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Title | GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI. | ||||||
![]() | PROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) | ||||||
![]() | LIGASE / GAR-SYN / GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE / ATP-GRASP / PURINE DE NOVO BIOSYNTHETIC PATHWAY / SUBSTRATE CHANNELING | ||||||
Function / homology | ![]() phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / DNA damage response / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, W. / Kappock, T.J. / Stubbe, J. / Ealick, S.E. | ||||||
![]() | ![]() Title: X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Authors: Wang, W. / Kappock, T.J. / Stubbe, J. / Ealick, S.E. #1: ![]() Title: Purification, Crystallization and Preliminary X-Ray Diffraction Data from Selenomethione Glycinamide Ribonucleotide Synthetase Authors: Weaver, T.M. / Wang, W. / Ealick, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.4 KB | Display | ![]() |
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Full document | ![]() | 420.4 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46283.527 Da / Num. of mol.: 1 / Mutation: P294L / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P15640, phosphoribosylamine-glycine ligase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1M MES PH6.3, 0.2M AMMONIUM SULFATE, 26% PEG 5K MONOMETHYLETHER, HANGING DROP VAPOR DEFFUSION, vapor diffusion - hanging drop | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Aug 1, 1997 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→20 Å / Num. obs: 58385 / % possible obs: 95.9 % / Redundancy: 5.2 % / Rsym value: 4.3 / Net I/σ(I): 10 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 17.4 / % possible all: 83.9 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.043 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 83.9 % / Num. unique obs: 7256 / Rmerge(I) obs: 0.174 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.6 Å / Rfactor Rfree: 0.307 / % reflection Rfree: 10 % / Rfactor Rwork: 0.298 |