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Open data
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Basic information
Entry | Database: PDB / ID: 1aj5 | ||||||
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Title | CALPAIN DOMAIN VI APO | ||||||
![]() | CALPAIN | ||||||
![]() | CALCIUM-BINDING PROTEIN / CALCIUM-DEPENDENT PROTEASE / APO FORM / SMALL SUBUNIT | ||||||
Function / homology | ![]() Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / protein catabolic process / calcium ion binding / protein-containing complex binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cygler, M. / Grochulski, P. / Blanchard, H. | ||||||
![]() | ![]() Title: Structure of a calpain Ca(2+)-binding domain reveals a novel EF-hand and Ca(2+)-induced conformational changes. Authors: Blanchard, H. / Grochulski, P. / Li, Y. / Arthur, J.S. / Davies, P.L. / Elce, J.S. / Cygler, M. #1: ![]() Title: Ca(2+)-Binding Domain Vi of Rat Calpain is a Homodimer in Solution: Hydrodynamic, Crystallization and Preliminary X-Ray Diffraction Studies Authors: Blanchard, H. / Li, Y. / Cygler, M. / Kay, C.M. / Arthur, J.S. / Davies, P.L. / Elce, J.S. #2: ![]() Title: Active Recombinant Rat Calpain II. Bacterially Produced Large and Small Subunits Associate Both in Vivo and in Vitro Authors: Graham-Siegenthaler, K. / Gauthier, S. / Davies, P.L. / Elce, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 438.7 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.055906, -0.998257, -0.018923), Vector: Details | THERE ARE TWO INDEPENDENT "PHYSIOLOGICAL" DIMERS OF THE SAME TYPE: AA' AND BB'. A AND A' ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ALONG THE X AXIS. B AND B' ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ALONG Y AXIS AND TRANSLATED BY VECTOR (1.0,0.0,0.5). THE DIMERS ARE RELATED BY THE NCS SYMMETRY. | |
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Components
#1: Protein | Mass: 20027.633 Da / Num. of mol.: 2 Fragment: SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: 38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 24, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 17172 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.19 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 80668 |
Reflection shell | *PLUS % possible obs: 94.2 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 33.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.28 |