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Yorodumi- PDB-3cxp: Crystal structure of human glucosamine 6-phosphate N-acetyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cxp | ||||||
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Title | Crystal structure of human glucosamine 6-phosphate N-acetyltransferase 1 mutant E156A | ||||||
Components | Glucosamine 6-phosphate N-acetyltransferase | ||||||
Keywords | TRANSFERASE / GNA1 / Acyltransferase / Endosome / Golgi apparatus / Membrane | ||||||
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 / endoplasmic reticulum / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Wang, J. / Liu, X. / Li, L.-F. / Su, X.-D. | ||||||
Citation | Journal: Febs Lett. / Year: 2008 Title: Acceptor substrate binding revealed by crystal structure of human glucosamine-6-phosphate N-acetyltransferase 1 Authors: Wang, J. / Liu, X. / Liang, Y.-H. / Li, L.-F. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cxp.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxp.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cxp_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 3cxp_full_validation.pdf.gz | 421.7 KB | Display | |
Data in XML | 3cxp_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 3cxp_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxp ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxp | HTTPS FTP |
-Related structure data
Related structure data | 3cxqC 3cxsC 2huzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20718.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNPNAT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q96EK6, glucosamine-phosphate N-acetyltransferase |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.1M K Thiocyanate, 30% w/v PEG MME 2000, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.0001 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 23, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 13549 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.437 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 42.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HUZ Resolution: 2.01→19.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.836 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.927 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.006→2.057 Å / Total num. of bins used: 20
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