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Yorodumi- PDB-5nzh: Crystal structure of UDP-glucose pyrophosphorylase V402W mutant f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nzh | ||||||
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Title | Crystal structure of UDP-glucose pyrophosphorylase V402W mutant from Leishmania major | ||||||
Components | UDP-glucose pyrophosphorylaseUTP—glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / NTP-transferase / Pathogen / Allostery / Catalysis | ||||||
Function / homology | Function and homology information UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / ciliary plasm / glycogen metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Hesse, R. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies Authors: Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nzh.cif.gz | 203.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nzh.ent.gz | 162.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzh ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzh | HTTPS FTP |
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-Related structure data
Related structure data | 5nzgC 5nziC 5nzjC 5nzkC 5nzlC 5nzmC 2oefS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 56141.852 Da / Num. of mol.: 2 / Mutation: V402W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: UGP, LMJF_18_0990 / Production host: Escherichia coli (E. coli) References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase #2: 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: 2.65 Å3/Da / Density % sol: 53.63 % / Mosaicity: 0.32 ° |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 2.25M ammonium sulfate, 100mM Tris-HCl pH 7.2, 0.1% Tween 80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.854 Å / Num. obs: 26339 / % possible obs: 99.9 % / Redundancy: 7.04 % / Biso Wilson estimate: 21.83 Å2 / Rsym value: 0.0183 / Net I/σ(I): 4.37 |
Reflection shell | Mean I/σ(I) obs: 2.14 / Rsym value: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OEF Resolution: 2.9→47.854 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.854 Å
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Refine LS restraints |
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LS refinement shell |
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