+Open data
-Basic information
Entry | Database: PDB / ID: 1yp2 | ||||||
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Title | Crystal structure of potato tuber ADP-glucose pyrophosphorylase | ||||||
Components | Glucose-1-phosphate adenylyltransferase small subunit | ||||||
Keywords | TRANSFERASE / ADP-glucose synthase / ADP-glucose pyrophosphorylase / AGPASE B / Alpha-D-glucose-1-phosphate adenyl transferase | ||||||
Function / homology | Function and homology information starch biosynthetic process / amyloplast / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / chloroplast / ATP binding Similarity search - Function | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å | ||||||
Authors | Jin, X. / Ballicora, M.A. / Preiss, J. / Geiger, J.H. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Crystal structure of potato tuber ADP-glucose pyrophosphorylase. Authors: Jin, X. / Ballicora, M.A. / Preiss, J. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yp2.cif.gz | 362.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yp2.ent.gz | 304.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/1yp2 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/1yp2 | 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: 49795.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pMLaugh10 / Production host: Escherichia coli (E. coli) / Strain (production host): AC70R1-504 References: UniProt: P23509, glucose-1-phosphate adenylyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PMB / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→20 Å / Num. all: 104777 / Num. obs: 84060 / % possible obs: 80.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.23 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.11→19.94 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 141491.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.7755 Å2 / ksol: 0.347561 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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