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Yorodumi- PDB-2oef: Open and Closed Structures of the UDP-Glucose Pyrophosphorylase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oef | ||||||
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Title | Open and Closed Structures of the UDP-Glucose Pyrophosphorylase from Leishmania major | ||||||
Components | UTP-glucose-1-phosphate uridylyltransferase 2, putativeUTP—glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann-fold / beta-helix / pyrophosphorylase | ||||||
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: 2.4 Å | ||||||
Authors | Steiner, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Open and Closed Structures of the UDP-glucose Pyrophosphorylase from Leishmania major. Authors: Steiner, T. / Lamerz, A.C. / Hess, P. / Breithaupt, C. / Krapp, S. / Bourenkov, G. / Huber, R. / Gerardy-Schahn, R. / Jacob, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oef.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oef.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oef ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oef | HTTPS FTP |
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-Related 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: 56945.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: UGP / Production host: Escherichia coli (E. coli) References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase | ||
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#2: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 21% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2005 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.95 Å / Num. all: 23509 / Num. obs: 21635 / % possible obs: 92.1 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.7 / Biso Wilson estimate: 33.6 Å2 |
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 409084.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3053 Å2 / ksol: 0.34843 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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