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- PDB-1u5i: Crystal Structure analysis of rat m-calpain mutant Lys10 Thr -

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Basic information

Entry
Database: PDB / ID: 1u5i
TitleCrystal Structure analysis of rat m-calpain mutant Lys10 Thr
Components
  • Calpain 2, large [catalytic] subunit precursor
  • Calpain small subunit 1
KeywordsHYDROLASE / calpain / sulfhydryl protease
Function / homology
Function and homology information


calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process ...calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / response to mechanical stimulus / cytoskeletal protein binding / proteolysis involved in protein catabolic process / cell projection / female pregnancy / cellular response to amino acid stimulus / protein catabolic process / response to hydrogen peroxide / peptidase activity / cellular response to lipopolysaccharide / lysosome / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / calcium ion binding / dendrite / protein-containing complex binding / chromatin / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Jelly Rolls - #380 / 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 ...CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Jelly Rolls - #380 / 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 / EF-hand / Recoverin; domain 1 / 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 / Jelly Rolls / Alpha-Beta Complex / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calpain-2 catalytic subunit / Calpain small subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsHosfield, C.M. / Pal, G.P. / Elce, J.S. / Jia, Z.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Activation of calpain by Ca2+: roles of the large subunit N-terminal and domain III-IV linker peptides
Authors: Hosfield, C.M. / Elce, J.S. / Jia, Z.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain 2, large [catalytic] subunit precursor
B: Calpain small subunit 1


Theoretical massNumber of molelcules
Total (without water)101,2712
Polymers101,2712
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.658, 156.520, 64.227
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calpain 2, large [catalytic] subunit precursor / m-calpain large subunit


Mass: 79965.961 Da / Num. of mol.: 1 / Mutation: K10T, C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07009, calpain-2
#2: Protein Calpain small subunit 1 / m-calpain small subunit


Mass: 21304.979 Da / Num. of mol.: 1 / Fragment: residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q64537
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 6000, MES, sodium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 1998 / Details: Osmic
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 2.63→25 Å / Num. all: 27000 / Num. obs: 25795 / % possible obs: 95 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.63→2.7 Å / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.89 / SU B: 13.288 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28333 1373 5.1 %RANDOM
Rwork0.19144 ---
obs0.19605 25795 90.09 %-
all-27000 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.171 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20 Å20.31 Å2
2--3.82 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6407 0 0 299 6706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0640.0216519
X-RAY DIFFRACTIONr_bond_other_d0.0090.025806
X-RAY DIFFRACTIONr_angle_refined_deg3.8911.9478786
X-RAY DIFFRACTIONr_angle_other_deg1.792313501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5435790
X-RAY DIFFRACTIONr_chiral_restr0.2530.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.027269
X-RAY DIFFRACTIONr_gen_planes_other0.0320.021387
X-RAY DIFFRACTIONr_nbd_refined0.3190.22227
X-RAY DIFFRACTIONr_nbd_other0.3010.28119
X-RAY DIFFRACTIONr_nbtor_other0.1330.24182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2930.2344
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.22
X-RAY DIFFRACTIONr_mcbond_it2.4921.53951
X-RAY DIFFRACTIONr_mcangle_it4.32926316
X-RAY DIFFRACTIONr_scbond_it6.07532568
X-RAY DIFFRACTIONr_scangle_it9.2354.52470
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.432 81
Rwork0.301 1907

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