+Open data
-Basic information
Entry | Database: PDB / ID: 1fxz | ||||||
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Title | CRYSTAL STRUCTURE OF SOYBEAN PROGLYCININ A1AB1B HOMOTRIMER | ||||||
Components | GLYCININ G1 | ||||||
Keywords | PLANT PROTEIN / Proglycinin / Glycinin / Legumin / Seed Storage Protein | ||||||
Function / homology | Function and homology information protein storage vacuole / nutrient reservoir activity / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Adachi, M. / Takenaka, Y. / Gidamis, A.B. / Mikami, B. / Utsumi, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of soybean proglycinin A1aB1b homotrimer. Authors: Adachi, M. / Takenaka, Y. / Gidamis, A.B. / Mikami, B. / Utsumi, S. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and preliminary X-ray Crystallographic analysis of the soybean proglycinin expressed in Escherichia coli. Authors: Utsumi, S. / Gidamis, A.B. / Mikami, B. / Kito, M. #2: Journal: Gene / Year: 1988 Title: Signal sequence of preproglycinin affects production of the expressed protein in Escherichia coli. Authors: Utsumi, S. / Kim, C.S. / Sato, T. / Kito, M. #3: Journal: J.Agric.Food Chem. / Year: 1987 Title: An alternate cDNA encoding glycinin A1aBx subunit Authors: Utsumi, S. / Kohno, T. / Mori, T. / Kito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fxz.cif.gz | 221.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fxz.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fxz_validation.pdf.gz | 387.4 KB | Display | wwPDB validaton report |
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Full document | 1fxz_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 1fxz_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 1fxz_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/1fxz ftp://data.pdbj.org/pub/pdb/validation_reports/fx/1fxz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer corresponding to that in asymmetric unit. |
-Components
#1: Protein | Mass: 53682.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Tissue: SEED / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04776 #2: 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: 3.04 Å3/Da / Density % sol: 59.59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 302 K / Method: dialysis / pH: 7.6 / Details: pH 7.6, Dialysis, temperature 302.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 281 K / pH: 5.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 68 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 17, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 142631 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 3.1 % |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. obs: 46010 / Num. measured all: 142631 / Rmerge(I) obs: 0.089 |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.199 / Rfactor Rfree: 0.25 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / Rfactor Rfree: 0.341 / Rfactor obs: 0.271 |