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Yorodumi- PDB-4bqh: Crystal structure of the uridine diphosphate N-acetylglucosamine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bqh | ||||||
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Title | Crystal structure of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei in complex with inhibitor | ||||||
Components | UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / INHIBITOR | ||||||
Function / homology | Function and homology information nucleotide-sugar biosynthetic process / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-alpha-D-glucose metabolic process / UDP-N-acetylglucosamine biosynthetic process / glycosome / nucleotidyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | TRYPANOSOMA BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Fang, W. / Raimi, O.G. / vanAalten, D.M.F. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: A Novel Allosteric Inhibitor of the Uridine Diphosphate N-Acetylglucosamine Pyrophosphorylase from Trypanosoma Brucei. Authors: Urbaniak, M.D. / Collie, I.T. / Fang, W. / Aristotelous, T. / Eskilsson, S. / Raimi, O.G. / Harrison, J. / Hopkins Navratolova, I. / Frearson, J.A. / Van Aalten, D.M.F. / Ferguson, M.A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bqh.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bqh.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bqh_validation.pdf.gz | 798.5 KB | Display | wwPDB validaton report |
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Full document | 4bqh_full_validation.pdf.gz | 803.1 KB | Display | |
Data in XML | 4bqh_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4bqh_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqh ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqh | HTTPS FTP |
-Related structure data
Related structure data | 1jv1S S: Starting model for refinement |
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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: 60598.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PGEX-6P-1-TBUAP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q386Q8, UDP-N-acetylglucosamine diphosphorylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-9VU / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.38 % / Description: NONE |
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Crystal grow | Details: 25% PEG3350, 0.2M (NH4)2SO4, 0.1 M BIS-TRIS PH5.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 58590 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.75→25 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.5 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JV1 Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.034 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.519 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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