+Open data
-Basic information
Entry | Database: PDB / ID: 3cxs | ||||||
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Title | Crystal structure of human GNA1 | ||||||
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: 2.7 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 | 3cxs.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxs.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxs ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxs | HTTPS FTP |
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-Related structure data
Related structure data | 3cxpC 3cxqC 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: 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: 2.12 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.2M MgCl2, 0.1M Bis-Tris pH 6.3, 25% w/v PEG 3350, vapor diffusion, hanging drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jan 15, 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: 2.7→50 Å / Num. all: 5481 / Num. obs: 5121 / % possible obs: 94.49 % / Redundancy: 5.53 % / Rsym value: 0.063 / Χ2: 0.73 / Net I/σ(I): 8.96 / Scaling rejects: 1374 | ||||||||||||||||||||||||||||||||||||
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: 2.7→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.86 / SU B: 17.374 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / 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: 35.282 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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