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- PDB-1i12: CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i12 | ||||||
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Title | CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA | ||||||
![]() | GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE | ||||||
![]() | TRANSFERASE / GNAT / ALPHA/BETA | ||||||
Function / homology | ![]() Synthesis of UDP-N-acetyl-glucosamine / glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peneff, C. / Mengin-Lecreulx, D. / Bourne, Y. | ||||||
![]() | ![]() Title: The crystal structures of Apo and complexed Saccharomyces cerevisiae GNA1 shed light on the catalytic mechanism of an amino-sugar N-acetyltransferase. Authors: Peneff, C. / Mengin-Lecreulx, D. / Bourne, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 153.8 KB | Display | ![]() |
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PDB format | ![]() | 122.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18259.021 Da / Num. of mol.: 4 / Mutation: S39C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YFL017C / Plasmid: PQE30 / Production host: ![]() ![]() References: UniProt: P43577, glucosamine-phosphate N-acetyltransferase #2: Chemical | ChemComp-ACO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 43.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: PEG 600, IMIDAZOLE, MALATE, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→26.82 Å / Num. all: 166110 / Num. obs: 547136 / % possible obs: 96.1 % / Observed criterion σ(I): 1.9 / Redundancy: 2.05 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.045 / Net I/σ(I): 7.9724 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 15590 / Rsym value: 0.376 / % possible all: 92.3 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 92.3 % / Rmerge(I) obs: 0.376 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.56 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→24.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 1.8 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.299 / % reflection Rfree: 1.7 % / Rfactor Rwork: 0.288 |