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Open data
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Basic information
Entry | Database: PDB / ID: 1dvi | ||||||
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Title | CALPAIN DOMAIN VI WITH CALCIUM BOUND | ||||||
![]() | CALPAIN | ||||||
![]() | CALCIUM-DEPENDENT PROTEASE / 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. / Blanchard, H. / Grochulski, P. | ||||||
![]() | ![]() 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 | ![]() | 90.5 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.2 KB | Display | ![]() |
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Full document | ![]() | 435 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.4 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (0.997267, -0.010967, -0.073069), Vector: |
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Components
#1: Protein | Mass: 21288.914 Da / Num. of mol.: 2 Fragment: SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 17% PEG 8K, 50MM CACODYLATE PH. 6.5 , 10% GLYCEROL, 200MM CACL2 | ||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42 Å / Num. obs: 16358 / % possible obs: 93.6 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.1 / % possible all: 85.5 |
Reflection | *PLUS Num. measured all: 57387 |
Reflection shell | *PLUS % possible obs: 85.5 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: NCS GROUP 1 COMPRISES OF HELICAL REGIONS, NCS GROUP 2 COMPRISES OF LOOP REGIONS
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Displacement parameters | Biso mean: 21.2 Å2
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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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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / 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: 0.22 |