+Open data
-Basic information
Entry | Database: PDB / ID: 2o28 | |||||||||
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Title | Crystal Structure of GNPNAT1 | |||||||||
Components | Glucosamine 6-phosphate N-acetyltransferase | |||||||||
Keywords | TRANSFERASE / ACETYLTRANSFERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC | |||||||||
Function / homology | Function and homology information glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine biosynthetic process / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / endosome membrane / Golgi membrane / Golgi apparatus / endoplasmic reticulum ...glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine biosynthetic process / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / endosome membrane / Golgi membrane / Golgi apparatus / endoplasmic reticulum / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Glucosamine-Phosphate N-Acetyltransferase 1 Authors: Wu, H. / Min, J. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o28.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o28.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 2o28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o28 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o28 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20776.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNPNAT1, GNA1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96EK6, glucosamine-phosphate N-acetyltransferase #2: Sugar | ChemComp-16G / | #3: Chemical | #4: 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: 2.44 Å3/Da / Density % sol: 49.61 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M BICINE pH 9.0, 27% PEG3350, 0.2M MgCl2, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.41 Å / Num. obs: 33633 / % possible obs: 89.7 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.248 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Total num. of bins used: 20
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