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Yorodumi- PDB-3brk: Crystal Structure of ADP-Glucose Pyrophosphorylase from Agrobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3brk | ||||||
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Title | Crystal Structure of ADP-Glucose Pyrophosphorylase from Agrobacterium tumefaciens | ||||||
Components | Glucose-1-phosphate adenylyltransferase | ||||||
Keywords | TRANSFERASE / ADP-glucose pyrophosphorylase / Agrobacterium tumefaciens / allostery / kinetics / structure-function relationships / site-directed mutagenesis / Glycogen biosynthesis / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Cupp-Vickery, J. / Meyer, C. / Igarashi, R. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural analysis of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens. Authors: Cupp-Vickery, J.R. / Igarashi, R.Y. / Perez, M. / Poland, M. / Meyer, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3brk.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3brk.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 3brk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/3brk ftp://data.pdbj.org/pub/pdb/validation_reports/br/3brk | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47509.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: glgC / Production host: Escherichia coli (E. coli) References: UniProt: P39669, glucose-1-phosphate adenylyltransferase | ||
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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: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 1.5M lithium sulfate, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
Detector | Detector: CCD / Date: Jun 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→79 Å / Num. all: 33214 / Num. obs: 33214 / % possible obs: 99.9 % / Rsym value: 0.069 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.9 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.4 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.297 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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