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Yorodumi- PDB-5nzi: Crystal structure of UDP-glucose pyrophosphorylase S374F mutant f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nzi | ||||||
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Title | Crystal structure of UDP-glucose pyrophosphorylase S374F mutant from Leishmania major in complex with UDP-glucose | ||||||
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: 2.05 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 | 5nzi.cif.gz | 207.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nzi.ent.gz | 166.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzi ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzi | HTTPS FTP |
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-Related structure data
Related structure data | 5nzgC 5nzhC 5nzjC 5nzkC 5nzlC 5nzmC 2m2aS 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
#1: Protein | Mass: 56114.863 Da / Num. of mol.: 1 / Mutation: S374F 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 | ||
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#2: Chemical | ChemComp-UPG / | ||
#3: Chemical | #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: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 24% PEG 3350, 100 mM Bis-Tris pH 6.8, 0.2 M Li2SO4, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 30193 / % possible obs: 98.5 % / Redundancy: 13.43 % / Rsym value: 0.055 / Net I/σ(I): 10.49 |
Reflection shell | Resolution: 2.05→2.15 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 3929 / Rsym value: 0.421 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2M2A Resolution: 2.05→44.756 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→44.756 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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