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Yorodumi- PDB-2vez: AfGNA1 crystal structure complexed with Acetyl-CoA and Glucose-6P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vez | ||||||
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Title | AfGNA1 crystal structure complexed with Acetyl-CoA and Glucose-6P gives new insights into catalysis | ||||||
Components | PUTATIVE GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ACYLTRANSFERASE / GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE (GNA1) UDP-GLCNAC BIOSYNTHETIC PATHWAY | ||||||
Function / homology | Function and homology information glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Hurtado-Guerrero, R. / Raimi, O. / Shepherd, S. / van Aalten, D.M.F. | ||||||
Citation | Journal: FEBS Lett. / Year: 2007 Title: Glucose-6-Phosphate as a Probe for the Glucosamine- 6-Phosphate N-Acetyltransferase Michaelis Complex. Authors: Hurtado-Guerrero, R. / Raimi, O. / Shepherd, S. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vez.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vez.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2vez ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2vez | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 21126.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PLYS References: UniProt: Q4WCU5, glucosamine-phosphate N-acetyltransferase |
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#2: Chemical | ChemComp-ACO / |
#3: Sugar | ChemComp-G6P / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 46.79 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. obs: 33822 / % possible obs: 94.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.447 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-25 ARE DISORDERED.
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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: 19.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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