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Yorodumi- PDB-5nzm: Crystal structure of UDP-glucose pyrophosphorylase from Leishmani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nzm | ||||||
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Title | Crystal structure of UDP-glucose pyrophosphorylase from Leishmania major in complex with murrayamine-I | ||||||
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: 2.35 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 | 5nzm.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nzm.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzm ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzm | HTTPS FTP |
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-Related structure data
Related structure data | 5nzgC 5nzhC 5nziC 5nzjC 5nzkC 5nzlC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56054.770 Da / Num. of mol.: 1 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-9ET / |
#3: 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: 2.93 Å3/Da / Density % sol: 58.05 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 2.25 M ammonium sulfate, 100 mM 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: ESRF / Beamline: ID30B / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 27167 / % possible obs: 100 % / Redundancy: 12.17 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.035 / Net I/σ(I): 15.98 |
Reflection shell | Resolution: 2.35→2.45 Å / Mean I/σ(I) obs: 2.38 / Num. unique obs: 3182 / Rsym value: 0.401 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OEF Resolution: 2.35→49.359 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→49.359 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.2494 Å / Origin y: 18.8266 Å / Origin z: -7.3975 Å
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Refinement TLS group | Selection details: all |