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Yorodumi- PDB-5oaw: Crystal structure of Aspergillus fumigatus N-acetylphosphoglucosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oaw | ||||||
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Title | Crystal structure of Aspergillus fumigatus N-acetylphosphoglucosamine mutase in complex with GlcNAc-6P and magnesium | ||||||
Components | Phosphoacetylglucosamine mutase | ||||||
Keywords | ISOMERASE / Mutase / N-acetylphosphoglucosamine / Aspergillus fumigatus | ||||||
Function / homology | Function and homology information phosphoacetylglucosamine mutase / phosphoacetylglucosamine mutase activity / UDP-N-acetylglucosamine biosynthetic process / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Aspergillus lentulus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.34 Å | ||||||
Authors | Raimi, O.G. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: Evidence for substrate-assisted catalysis inN-acetylphosphoglucosamine mutase. Authors: Raimi, O.G. / Hurtado-Guerrero, R. / 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 | 5oaw.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oaw.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 5oaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oaw_validation.pdf.gz | 997.1 KB | Display | wwPDB validaton report |
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Full document | 5oaw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5oaw_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 5oaw_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/5oaw ftp://data.pdbj.org/pub/pdb/validation_reports/oa/5oaw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 60008.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Serine is phosphorylated / Source: (gene. exp.) Aspergillus lentulus (mold) / Gene: ALT_8497 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLysS References: UniProt: A0A0S7E9S6, phosphoacetylglucosamine mutase #2: Chemical | ChemComp-MG / | #3: Sugar | #4: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 1000, 100 mM HEPES, pH 7.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→20 Å / Num. obs: 48393 / % possible obs: 99.8 % / Redundancy: 3.5 % / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 2.35→2.43 Å |
-Processing
Software |
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Refinement | Resolution: 2.34→93.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.002 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 51.666 Å2
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Refinement step | Cycle: 1 / Resolution: 2.34→93.25 Å
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Refine LS restraints |
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