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Yorodumi- PDB-2pa4: Crystal structure of UDP-glucose pyrophosphorylase from Corynebac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pa4 | ||||||
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Title | Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose | ||||||
Components | UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASEUTP—glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / phosphorylase / nucleotidyltransferase / metabolism | ||||||
Function / homology | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / URIDINE-5'-DIPHOSPHATE-GLUCOSE / : Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Active site geometry of glucose-1-phosphate uridylyltransferase. Authors: Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pa4.cif.gz | 252 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pa4.ent.gz | 202.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pa4 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pa4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a homo-tetramer comprised of chains A, B, C, and D as deposited in the pdb entry |
-Components
#1: Protein | Mass: 34780.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Species: Corynebacterium glutamicum / Strain: ATCC-13032 / Gene: galU1 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q6M6R3, UTP-glucose-1-phosphate uridylyltransferase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-UPG / #4: 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: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 23% PEG-3400, 200 mM MgCl2, 200 mM NaCl, 10 mM UDP-glucose, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99848 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2006 / Details: mirrors |
Radiation | Monochromator: Double-crystal monochromater Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99848 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 78712 / Num. obs: 78712 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5571 / Rsym value: 0.198 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2→20 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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