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- PDB-1kxr: Crystal Structure of Calcium-Bound Protease Core of Calpain I -

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Basic information

Entry
Database: PDB / ID: 1kxr
TitleCrystal Structure of Calcium-Bound Protease Core of Calpain I
Componentsthiol protease DOMAINS I AND II
KeywordsHYDROLASE / PAPAIN-RELATED / CALCIUM-DEPENDENT CYSTEINE PROTEASE / TWO NOVEL COOPERATIVE CALCIUM SITES
Function / homology
Function and homology information


calpain-1 / Degradation of the extracellular matrix / regulation of catalytic activity / protein catabolic process at postsynapse / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / negative regulation of actin filament polymerization / self proteolysis / cornified envelope ...calpain-1 / Degradation of the extracellular matrix / regulation of catalytic activity / protein catabolic process at postsynapse / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / receptor catabolic process / positive regulation of vascular permeability / response to angiotensin / response to arsenic-containing substance / negative regulation of non-canonical NF-kappaB signal transduction / Neutrophil degranulation / protein autoprocessing / positive regulation of cardiac muscle cell apoptotic process / cytoskeletal protein binding / protein catabolic process / cellular response to hydrogen peroxide / peptidase activity / presynapse / lysosome / postsynapse / postsynaptic density / calcium ion binding / glutamatergic synapse / enzyme binding / mitochondrion / proteolysis / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. ...Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. / Calpain-like thiol protease family. / EF-hand domain pair / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMoldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: A Ca(2+) switch aligns the active site of calpain.
Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L.
History
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.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.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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thiol protease DOMAINS I AND II
B: thiol protease DOMAINS I AND II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7376
Polymers77,5772
Non-polymers1604
Water6,467359
1
A: thiol protease DOMAINS I AND II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8693
Polymers38,7881
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thiol protease DOMAINS I AND II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8693
Polymers38,7881
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.443, 40.492, 132.328
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein thiol protease DOMAINS I AND II / calpain I protease core


Mass: 38788.488 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-356 / Mutation: C115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CAPN1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P97571, EC: 3.4.22.17
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium chloride, calcium chloride, MES, PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.5 M1reservoirNaCl
22 %PEG60001reservoir
30.1 MMES1reservoirpH6.0
415 %glycerol1reservoir
510 mM1reservoirCaCl2
612.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→30 Å / Num. obs: 43051 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.3
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4388 / Rsym value: 0.368 / % possible all: 94.6
Reflection
*PLUS
% possible obs: 92 % / Num. measured all: 119331
Reflection shell
*PLUS
Rmerge(I) obs: 0.14

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DF0

1df0


Resolution: 2.07→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2154 -RANDOM
Rwork0.213 ---
obs-43051 92 %-
Refinement stepCycle: LAST / Resolution: 2.07→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 4 359 5517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.07-2.140.27331910.2432X-RAY DIFFRACTION3859
2.14-2.230.27572200.2319X-RAY DIFFRACTION4167
2.23-2.330.25772330.2337X-RAY DIFFRACTION4138
2.33-2.450.27232120.2221X-RAY DIFFRACTION4187
2.45-2.610.28462680.2239X-RAY DIFFRACTION4151
2.61-2.810.25761920.2141X-RAY DIFFRACTION4170
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.232
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor obs: 0.2432

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