+Open data
-Basic information
Entry | Database: PDB / ID: 1i1d | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P | ||||||
Components | GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALPHA/BETA / DOMAIN SWAPPING / GNAT CONSERVED CORE | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Peneff, C. / Mengin-Lecreulx, D. / Bourne, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i1d.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i1d.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i1d_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1i1d_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1i1d_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 1i1d_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1d ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1d | HTTPS FTP |
-Related structure data
Related structure data | 1i12SC 1i21C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 18316.074 Da / Num. of mol.: 4 / Mutation: S39C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YFL017C / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP 4) References: UniProt: P43577, glucosamine-phosphate N-acetyltransferase #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: PEG 600, IMIDAZOLE/MALATE, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.1 / Wavelength: 1.1 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1999 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. obs: 62765 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 4.8 / Net I/σ(I): 12.5 | |||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 41.2 / % possible all: 96.3 | |||||||||
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.048 | |||||||||
Reflection shell | *PLUS % possible obs: 96.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I12 Resolution: 1.8→24.12 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1131451.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.22 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / 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 σ(F): 0 / % reflection Rfree: 1.8 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.8 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / % reflection Rfree: 1.7 % / Rfactor Rwork: 0.259 |