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Yorodumi- PDB-3kih: The crystal structures of two fragments truncated from 5-bladed b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kih | |||||||||
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Title | The crystal structures of two fragments truncated from 5-bladed beta-propeller lectin, tachylectin-2 (Lib2-D2-15) | |||||||||
Components | 5-bladed beta-propeller lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / 5-bladed beta-propeller / Structural Genomics / Israel Structural Proteomics Center / ISPC | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Dym, O. / Tawfik, D.S. / Yadid, I. / Israel Structural Proteomics Center (ISPC) | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Metamorphic proteins mediate evolutionary transitions of structure Authors: Yadid, I. / Kirshenbaum, N. / Sharon, M. / Dym, O. / Tawfik, D.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kih.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kih.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kih_validation.pdf.gz | 476.1 KB | Display | wwPDB validaton report |
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Full document | 3kih_full_validation.pdf.gz | 484.5 KB | Display | |
Data in XML | 3kih_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3kih_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/3kih ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3kih | HTTPS FTP |
-Related structure data
Related structure data | 3kifC 1tl2S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 10818.021 Da / Num. of mol.: 5 / Fragment: residues 1-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pETtr / Production host: Escherichia coli (E. coli) / References: UniProt: Q27084*PLUS #2: Sugar | ChemComp-GDL / #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 7 Details: 100mM HEPES, 0.2M magnesium chloride, 20% PEG 6000, pH 7, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 6, 2009 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 17718 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TL2 Resolution: 2.49→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.608 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.846 / ESU R Free: 0.359 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.555 Å / Total num. of bins used: 20
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