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Yorodumi- PDB-2vxk: Structural comparison between Aspergillus fumigatus and human GNA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vxk | ||||||
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Title | Structural comparison between Aspergillus fumigatus and human GNA1 | ||||||
Components | GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / KINETICS / UDP-GLCNAC / INHIBITOR DESIGN | ||||||
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 / SAD / Resolution: 1.8 Å | ||||||
Authors | Hurtado-Guerrero, R. / Raimi, O.G. / Min, J. / Zeng, H. / Vallius, L. / Shepherd, S. / Ibrahim, A.F.M. / Wu, H. / Plotnikov, A.N. / van Aalten, D.M.F. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Structural and Kinetic Differences between Human and Aspergillus Fumigatus D-Glucosamine-6- Phosphate N-Acetyltransferase. Authors: Hurtado-Guerrero, R. / Raimi, O.G. / Min, J. / Zeng, H. / Vallius, L. / Shepherd, S. / Ibrahim, A.F.M. / Wu, H. / Plotnikov, A.N. / 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 | 2vxk.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vxk.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vxk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2vxk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2vxk_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2vxk_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vxk ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxk | HTTPS FTP |
-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: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: Q4WCU5, glucosamine-phosphate N-acetyltransferase |
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#2: Sugar | ChemComp-16G / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-COA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.27 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 10 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 18376 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 10.5 / % possible all: 98 |
-Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.622 / SU ML: 0.081 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA IS NOT COMPLETE MODELLED SINCE AT THE END OF THE MOLECULE (REGION OF THE THIOL GROUP) WAS COMPLETELY 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: 12.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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