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- PDB-1dvi: CALPAIN DOMAIN VI WITH CALCIUM BOUND -

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Basic information

Entry
Database: PDB / ID: 1dvi
TitleCALPAIN DOMAIN VI WITH CALCIUM BOUND
ComponentsCALPAIN
KeywordsCALCIUM-DEPENDENT PROTEASE / 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 / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCygler, M. / Blanchard, H. / Grochulski, P.
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 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALPAIN
B: CALPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,89810
Polymers42,5782
Non-polymers3218
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-109 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 87.400, 118.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.997267, -0.010967, -0.073069), (0.006032, 0.997707, -0.067414), (0.07364, 0.066789, 0.995046)
Vector: -15.2806, 12.4468, -64.905)

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Components

#1: Protein CALPAIN /


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


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %PEG800011
250 mMcacodylate11
310 %glycerol11
4200 mM11CaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 1996 / Details: COLLIMATOR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
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: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: NCS GROUP 1 COMPRISES OF HELICAL REGIONS, NCS GROUP 2 COMPRISES OF LOOP REGIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1605 10 %RANDOM
Rwork0.206 ---
obs0.206 16005 93.6 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 8 196 3014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.691.5
X-RAY DIFFRACTIONx_mcangle_it2.652
X-RAY DIFFRACTIONx_scbond_it2.272
X-RAY DIFFRACTIONx_scangle_it3.522.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINED3.30.123100
226.40.28450
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 243 10 %
Rwork0.22 2188 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3CA-PARAM19.IONCA-TOP19.ION
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_deg20.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43
LS refinement shell
*PLUS
Rfactor obs: 0.22

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