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Yorodumi- PDB-4m28: UDP-Glucose Pyrophosphorylase from Leishmania major in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m28 | ||||||
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Title | UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp | ||||||
Components | UDP-glucose pyrophosphorylase | ||||||
Keywords | TRANSFERASE / UDP-glucose pyrophosphorylase / nucleotidyltransferase / Rossmann-like alpha/beta/alpha sandwich fold | ||||||
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: 3 Å | ||||||
Authors | Fuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
Citation | Journal: ACS CATALYSIS / Year: 2013 Title: Catalytic mechanism and allosteric regulation of UDP-glucose pyrophosphorylase from Leishmania major Authors: Fuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / 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 | 4m28.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m28.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 4m28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/4m28 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m28 | HTTPS FTP |
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-Related structure data
Related structure data | 2oefS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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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-UPC / |
#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: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1 M MES, 20% w/v PEG-4000, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2013 Details: monochromator (horizontally side diffracting Silicon 111 crystal). |
Radiation | Monochromator: monochromator (horizontally side diffracting Silicon 111 crystal). Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3→47.3 Å / Num. all: 126117 / Num. obs: 11151 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 70 Å2 / Rsym value: 8 / Net I/σ(I): 11.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2OEF Resolution: 3→47.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.525 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 84.193 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→47.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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