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Yorodumi- PDB-1ij6: CA2+-BOUND STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ij6 | ||||||
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Title | CA2+-BOUND STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM TRUE SLIME MOLD | ||||||
Components | PLASMODIAL SPECIFIC LAV1-2 PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / FOURTY KDA CALCIUM BINDING PROTEIN / CBP40 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Physarum polycephalum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Iwasaki, W. / Sasaki, H. / Nakamura, A. / Kohama, K. / Tanokura, M. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Metal-Free and Ca(2+)-Bound Structures of a Multidomain EF-Hand Protein, CBP40, from the Lower Eukaryote Physarum polycephalum Authors: Iwasaki, W. / Sasaki, H. / Nakamura, A. / Kohama, K. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ij6.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ij6.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ij6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ij6 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ij6 | 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: 37137.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physarum polycephalum (eukaryote) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: P14725 |
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#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Ammonium Sulfate, Calcium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Details: Iwasaki, W., (1999) J.Biochem., 126, 7. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 22, 1997 / Details: focusing mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→38.1 Å / Num. all: 13647 / Num. obs: 34014 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 3.12→3.23 Å / Rmerge(I) obs: 0.342 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 13647 / Num. measured all: 34014 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.38 |