+Open data
-Basic information
Entry | Database: PDB / ID: 2ds2 | ||||||
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Title | Crystal structure of mabinlin II | ||||||
Components |
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Keywords | PLANT PROTEIN / SEED STORAGE PROTEIN / SWEET PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Capparis masaikai (plant) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Li, D.F. / Zhu, D.Y. / Wang, D.C. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2008 Title: Crystal structure of Mabinlin II: a novel structural type of sweet proteins and the main structural basis for its sweetness. Authors: Li, D.F. / Jiang, P. / Zhu, D.Y. / Hu, Y. / Max, M. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ds2.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ds2.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ds2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ds2_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 2ds2_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 2ds2_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2ds2_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/2ds2 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/2ds2 | 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4174.806 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capparis masaikai (plant) / Tissue: SEED / References: UniProt: P30233 #2: Protein | Mass: 8327.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capparis masaikai (plant) / Tissue: SEED / References: UniProt: P30233 #3: Chemical | ChemComp-ACY / | #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: 1.6 Å3/Da / Density % sol: 24.5 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: SODIUM MALONATE, SODIUM ACETATE , pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 25, 2005 |
Radiation | Monochromator: CON-FOCUSE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20.5 Å / Num. obs: 17686 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.266 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.7→20.35 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029
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