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Yorodumi- PDB-6g9v: Crystal structure of Aspergillus fumigatus UDP-N-acetylglucosamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g9v | ||||||
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Title | Crystal structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase(AfUAP1) in complex with UDPGlcNAc, pyrophosphate and Mg2+ | ||||||
Components | UDP-N-acetylglucosamine pyrophosphorylase | ||||||
Keywords | TRANSFERASE / cell wall / anti fungal / pyrophosphorylase / Aspergillus fumigatus | ||||||
Function / homology | Function and homology information sporulation / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Raimi, O.G. / Hurtado-Guerrero, R. / Borodin, V. / Urbaniak, M. / Ferguson, M. / van Aalten, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: RSC Chem. Biol. / Year: 2020 Title: A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor Authors: Raimi, O.G. / Hurtado-Guerrero, R. / Borodkin, V. / Ferenbach, A. / Urbaniak, M.D. / Ferguson, M.A.J. / 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 | 6g9v.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g9v.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/6g9v ftp://data.pdbj.org/pub/pdb/validation_reports/g9/6g9v | HTTPS FTP |
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-Related structure data
Related structure data | 6g9wC 2yqsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56793.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_7G02180 / Production host: Escherichia coli (E. coli) References: UniProt: Q4WAR0, UDP-N-acetylglucosamine diphosphorylase #2: Chemical | ChemComp-UD1 / | #3: Chemical | ChemComp-PPV / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate and 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 113044 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.568 / Num. unique obs: 11144 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YQS Resolution: 1.75→19.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.499 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.261 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→19.97 Å
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Refine LS restraints |
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