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- PDB-2ary: Catalytic domain of Human Calpain-1 -

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Basic information

Entry
Database: PDB / ID: 2ary
TitleCatalytic domain of Human Calpain-1
ComponentsCalpain-1 catalytic subunit
KeywordsHYDROLASE / CYSTEINE PROTEASE / PAPAIN / CALCIUM-DEPENDENT / THIOL PROTEASE / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity ...calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / peptidase activity / ficolin-1-rich granule lumen / lysosome / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of cell population proliferation / mitochondrion / proteolysis / extracellular exosome / extracellular region / 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
BETA-MERCAPTOETHANOL / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalker, J.R. / Davis, T. / Lunin, V. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Davis, T. / Lunin, V. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structures of Human Calpains 1 and 9 Imply Diverse Mechanisms of Action and Auto-inhibition
Authors: Davis, T.L. / Walker, J.R. / Finerty, P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S.
History
DepositionAug 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_leaving_atom_flag / _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_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-1 catalytic subunit
B: Calpain-1 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5529
Polymers79,1572
Non-polymers3957
Water4,125229
1
A: Calpain-1 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7374
Polymers39,5781
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calpain-1 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8155
Polymers39,5781
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.534, 90.534, 433.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Calpain-1 catalytic subunit / / Calpain-1 large subunit / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / ...Calpain-1 large subunit / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / muCANP / Micromolar-calpain


Mass: 39578.465 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 33-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN1, CANPL1 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07384, calpain-1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.39 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 298 K / pH: 7.75
Details: 1.5 M Ammononium Formate, 0.1 M Tris pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97889
DetectorType: SBC-3 / Detector: CCD / Date: Aug 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.4→44.32 Å / Num. obs: 42153 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.56
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.44 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TLO

1tlo


Resolution: 2.4→44.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.352 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26387 2106 5 %RANDOM
Rwork0.21955 ---
obs0.22174 39890 98.83 %-
all-41996 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.488 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 4 241 5387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9427154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.062256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72615876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.51532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024056
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22401
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23583
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40433259
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35145108
X-RAY DIFFRACTIONr_scbond_it2.57152362
X-RAY DIFFRACTIONr_scangle_it3.87172046
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 146 -
Rwork0.317 2707 -
obs--93.73 %

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