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Yorodumi- PDB-6tdg: Crystal structure of Aspergillus fumigatus Glucosamine-6-phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tdg | ||||||
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Title | Crystal structure of Aspergillus fumigatus Glucosamine-6-phosphate N-acetyltransferase 1 in complex with compound 2 | ||||||
Components | Glucosamine 6-phosphate N-acetyltransferase | ||||||
Keywords | TRANSFERASE / fragment screening / anti fungal / Aspergillus fumigatus / inhibitor | ||||||
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 Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Raimi, O.G. / Stanley, M. / Lockhart, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Targeting a critical step in fungal hexosamine biosynthesis. Authors: Lockhart, D.E.A. / Stanley, M. / Raimi, O.G. / Robinson, D.A. / Boldovjakova, D. / Squair, D.R. / Ferenbach, A.T. / Fang, W. / 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 | 6tdg.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tdg.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tdg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6tdg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6tdg_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 6tdg_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/6tdg ftp://data.pdbj.org/pub/pdb/validation_reports/td/6tdg | HTTPS FTP |
-Related structure data
Related structure data | 6tdfC 6tdhC 2vezS 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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Unit cell |
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Components on special symmetry positions |
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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 Af293 (mold) / Gene: AFUA_6G02460 / Production host: Escherichia coli (E. coli) References: UniProt: Q4WCU5, glucosamine-phosphate N-acetyltransferase |
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#2: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-N3W / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1. 10% peg 1000, 10% peg 8000 2. 30% peg 1500 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→57.7 Å / Num. obs: 20528 / % possible obs: 97 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rsym value: 0.041 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.74→1.77 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26623 / CC1/2: 0.99 / Rsym value: 0.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vez Resolution: 1.74→57.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.717 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.54 Å2 / Biso mean: 33.054 Å2 / Biso min: 21.29 Å2
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Refinement step | Cycle: final / Resolution: 1.74→57.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.741→1.786 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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