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- PDB-1aj5: CALPAIN DOMAIN VI APO -

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Basic information

Entry
Database: PDB / ID: 1aj5
TitleCALPAIN DOMAIN VI APO
ComponentsCALPAIN
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM-DEPENDENT PROTEASE / APO FORM / SMALL SUBUNIT
Function / homology
Function and homology information


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
EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calpain small subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsCygler, M. / Grochulski, P. / Blanchard, H.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
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: Journal: Protein Sci. / Year: 1996
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: Journal: J.Biol.Chem. / Year: 1994
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
DepositionMay 15, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALPAIN
B: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water2,162120
1
A: CALPAIN

A: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4140 Å2
ΔGint-21 kcal/mol
Surface area15940 Å2
MethodPISA, PQS
2
B: CALPAIN

B: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3940 Å2
ΔGint-26 kcal/mol
Surface area16320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.500, 73.000, 156.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.055906, -0.998257, -0.018923), (0.995796, 0.057125, -0.071606), (0.072562, -0.01484, 0.997253)
Vector: 69.2975, -34.1384, -40.8175)
DetailsTHERE 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 CALPAIN /


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.) Rattus norvegicus (Norway rat) / Strain: BL21 (DE3) / Cell line: BL21 / Gene: CAPN4 / Organ: LIVER / Plasmid: PT7-7F-21K / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q64537
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.8
Details: 38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate11
21
31
41

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 24, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHASESphasing
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: NCS USED ONLY AT THE EARLY STAGE OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1636 9.9 %RANDOM
Rwork0.22 ---
obs0.22 16470 96.5 %-
Displacement parametersBiso mean: 33.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 120 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.081.5
X-RAY DIFFRACTIONx_mcangle_it4.532
X-RAY DIFFRACTIONx_scbond_it3.612
X-RAY DIFFRACTIONx_scangle_it5.042.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 258 9.9 %
Rwork0.28 2340 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Rfactor obs: 0.28

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