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Yorodumi- PDB-3cxq: Crystal structure of human glucosamine 6-phosphate N-acetyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cxq | ||||||
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Title | Crystal structure of human glucosamine 6-phosphate N-acetyltransferase 1 bound to GlcN6P | ||||||
Components | Glucosamine 6-phosphate N-acetyltransferase | ||||||
Keywords | TRANSFERASE / glucosamine 6-phosphate N-acetyltransferase 1 / 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 / endosome membrane / Golgi membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 | 3cxq.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxq.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxq ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxq | HTTPS FTP |
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-Related structure data
Related structure data | 3cxpC 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
#1: Protein | Mass: 20776.117 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: Sugar | ChemComp-GLP / |
#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: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Na formate, 25% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 3, 2008 / Details: Montel mirrors | |||||||||||||||||||||||||||
Radiation | Monochromator: Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→54.348 Å / Num. obs: 8884 / % possible obs: 90.38 % / Redundancy: 6.04 % / Rsym value: 0.063 / Χ2: 0.77 / Net I/σ(I): 9.2 / Scaling rejects: 109 | |||||||||||||||||||||||||||
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: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.536 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.263 / 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: 25.641 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.358 Å / Total num. of bins used: 20
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