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- PDB-2i7a: Domain IV of Human Calpain 13 -

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Basic information

Entry
Database: PDB / ID: 2i7a
TitleDomain IV of Human Calpain 13
ComponentsCalpain 13
KeywordsHYDROLASE / calpain / calcium-dependent cytoplasmic cysteine proteinases / papain-like / EF-hand / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / Degradation of the extracellular matrix / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / calcium ion binding / negative regulation of apoptotic process / proteolysis / cytoplasm
Similarity search - Function
Calpain-13 / 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 ...Calpain-13 / 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 / Recoverin; domain 1 / Papain-like cysteine peptidase superfamily / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calpain-13 / Calpain-13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalker, J.R. / Ng, K. / Davis, T.L. / Ravulapalli, R. / Butler-cole, C. / Finerty Jr., P.J. / Newman, E.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. ...Walker, J.R. / Ng, K. / Davis, T.L. / Ravulapalli, R. / Butler-cole, C. / Finerty Jr., P.J. / Newman, E.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human Calpain 13
Authors: Walker, J.R. / Ng, K. / Davis, T.L. / Ravulapalli, R. / Butler-Cole, C. / Finerty Jr., P.J. / Newman, E.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 30, 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4457
Polymers19,9291
Non-polymers5166
Water1,65792
1
A: Calpain 13
hetero molecules

A: Calpain 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,89114
Polymers39,8582
Non-polymers1,03312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5820 Å2
ΔGint-134 kcal/mol
Surface area15510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.115, 86.115, 47.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-6-

SO4

21A-15-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: Y, X, -Z

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Components

#1: Protein Calpain 13 /


Mass: 19928.982 Da / Num. of mol.: 1 / Fragment: residues 515-669
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN13 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q17RF0, UniProt: Q6MZZ7*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG4K, 0.2M NH4SO4, 0.1M Na-Ac, 10 mg/mL protein solution, cryoprotected with 25% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 18, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→19 Å / Num. all: 18860 / Num. obs: 18860 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rsym value: 0.091 / Net I/σ(I): 33.18
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1684 / Rsym value: 0.88 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KFU

1kfu


Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.039 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19699 952 5 %RANDOM
Rwork0.16918 ---
obs0.17054 17908 98.91 %-
all-18860 --
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: 37.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 27 92 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221325
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9931788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8775158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48623.55959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18715245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3221510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02958
X-RAY DIFFRACTIONr_nbd_refined0.2220.2616
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.296
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.217
X-RAY DIFFRACTIONr_mcbond_it2.1043813
X-RAY DIFFRACTIONr_mcangle_it2.66841270
X-RAY DIFFRACTIONr_scbond_it3.6545581
X-RAY DIFFRACTIONr_scangle_it4.8687518
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 66 -
Rwork0.31 1131 -
obs--86.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4403-1.6526-1.26675.7797-0.69722.3780.24280.8913-0.7209-0.7353-0.41210.06560.1062-0.00960.16920.03230.085-0.03230.0358-0.1317-0.008423.97621.911-14.206
218.7642-12.1373-10.76738.84710.915521.847-1.178-1.2188-1.60731.24170.08081.30761.62520.27521.09720.0221-0.01190.0649-0.14390.10020.097923.43117.419-1.527
36.8005-0.3386-1.41525.3607-1.68064.32070.31140.19020.0253-0.068-0.15890.2891-0.19530.125-0.15260.010.03910.00770.0166-0.027-0.036523.32631.065-7.16
412.2995-9.97352.443116.2026-3.32914.13980.69631.25340.0658-1.0326-0.6977-0.098-0.28790.11340.00130.06420.11980.05360.114-0.0134-0.169228.66331.006-17.284
52.9710.11391.19082.3181.528714.58760.17530.3027-0.0113-0.25330.0611-0.2044-0.13750.2038-0.2363-0.03150.02390.0332-0.0114-0.02820.004135.13224.995-6.938
64.0278-1.534-0.19386.0991-2.658912.6659-0.0265-0.2643-0.57560.14930.17430.32210.9086-0.0669-0.14780.00390.00790.0056-0.06860.0315-0.00633.76318.85.896
77.08880.4512-2.34562.8306-3.16716.0425-0.2741-0.4508-0.13630.24660.1189-0.1682-0.1768-0.18290.1551-0.03270.0435-0.02020.029-0.0094-0.075235.05626.10411.14
83.90580.3035-1.36189.14227.007112.90530.0370.28730.08280.0070.0778-0.63740.07420.1554-0.1148-0.07330.0117-0.03170.03410.02570.025340.83534.8592.863
922.695.63524.333234.27493.860516.135-0.1024-1.5120.41550.97360.0787-0.1153-0.2695-0.04180.0237-0.00870.0136-0.05810.0864-0.0146-0.08532.73638.98814.786
103.5781-1.8214-0.42743.98642.0924.0066-0.0584-0.3875-0.38470.39320.07330.25930.179-0.2142-0.0149-0.02950.0139-0.00390.03540.0427-0.034925.07328.7119.079
112.7947-0.0805-0.62811.6079-2.12924.1107-0.23470.20740.43060.1010.1556-0.5105-0.07410.050.079-0.0550.0044-0.0525-0.01670.0250.019334.17338.991-0.707
129.5595-1.66670.16634.7589-2.65163.1903-0.26880.16440.88550.03840.108-1.1592-0.34380.05980.1608-0.1085-0.0672-0.0507-0.09040.07410.247836.56252.401-2.005
132.95740.8905-0.465210.06752.00983.16-0.11920.33420.3491-0.21150.0306-0.3048-0.0190.18780.0886-0.0832-0.0322-0.02860.09530.051-0.040823.87747.004-5.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA507 - 52712 - 32
2X-RAY DIFFRACTION2AA528 - 53733 - 42
3X-RAY DIFFRACTION3AA538 - 55243 - 57
4X-RAY DIFFRACTION4AA553 - 56458 - 69
5X-RAY DIFFRACTION5AA565 - 57270 - 77
6X-RAY DIFFRACTION6AA573 - 58578 - 90
7X-RAY DIFFRACTION7AA586 - 59991 - 104
8X-RAY DIFFRACTION8AA600 - 607105 - 112
9X-RAY DIFFRACTION9AA608 - 612113 - 117
10X-RAY DIFFRACTION10AA613 - 634118 - 139
11X-RAY DIFFRACTION11AA635 - 646140 - 151
12X-RAY DIFFRACTION12AA647 - 658152 - 163
13X-RAY DIFFRACTION13AA659 - 669164 - 174

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