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- PDB-4phn: The Structural Basis of Differential Inhibition of Human Calpain ... -

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Basic information

Entry
Database: PDB / ID: 4phn
TitleThe Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / Calcium Binding / Protease
Function / homology
Function and homology information


Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsAllemann, R.K. / Rizkallah, P.J. / Adams, S.E. / Miller, D.J. / Hallett, M.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701192 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The structural basis of differential inhibition of human calpain by indole and phenyl alpha-mercaptoacrylic acids.
Authors: Adams, S.E. / Rizkallah, P.J. / Miller, D.J. / Robinson, E.J. / Hallett, M.B. / Allemann, R.K.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Other
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain small subunit 1
B: Calpain small subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,08810
Polymers39,7672
Non-polymers3218
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-121 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.530, 70.560, 58.670
Angle α, β, γ (deg.)90.00, 108.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calpain small subunit 1 / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent ...CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent protease small subunit / CDPS / Calcium-dependent protease small subunit 1 / Calpain regulatory subunit


Mass: 19883.477 Da / Num. of mol.: 2 / Fragment: PEF(S) domain VI, residues 94-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPNS1, CAPN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04574
#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


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG6000, 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.79→39.05 Å / Num. all: 35505 / Num. obs: 35505 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.6
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ALV

1alv


Resolution: 1.79→39.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.773 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22826 1777 5 %RANDOM
Rwork0.18348 ---
obs0.18577 33708 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.7 Å2
2---0.68 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.79→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 8 282 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192862
X-RAY DIFFRACTIONr_bond_other_d0.0010.022670
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.943852
X-RAY DIFFRACTIONr_angle_other_deg1.08536128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23924.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63715516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4841520
X-RAY DIFFRACTIONr_chiral_restr0.1560.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6831.7011392
X-RAY DIFFRACTIONr_mcbond_other1.6841.7011391
X-RAY DIFFRACTIONr_mcangle_it2.4952.541740
X-RAY DIFFRACTIONr_mcangle_other2.4942.541741
X-RAY DIFFRACTIONr_scbond_it2.3251.9591470
X-RAY DIFFRACTIONr_scbond_other2.3191.9591469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5332.8362112
X-RAY DIFFRACTIONr_long_range_B_refined6.38115.0173704
X-RAY DIFFRACTIONr_long_range_B_other6.31914.373570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 137 -
Rwork0.302 2535 -
obs--99.93 %
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)
12.9909-0.19980.68381.105-0.05861.49890.0226-0.12220.14360.01050.04150.1333-0.0478-0.0804-0.06410.0075-0.00660.00780.03550.02530.076-19.2049-7.2706-12.441
21.67030.03590.94011.5628-0.04832.48420.0682-0.0534-0.08640.1388-0.0754-0.01610.3647-0.09270.00720.08910.01220.01210.0909-0.01520.0458-3.9272-25.4895-11.0183
31.9335-1.0737-0.90512.464-1.7853.22570.3005-0.3656-0.2182-0.0985-0.00970.4419-0.22240.4322-0.29080.1171-0.0637-0.01120.1073-0.01040.139-20.3906-9.7718-6.548
41.0064-0.1569-0.41610.7155-0.24640.3124-0.14160.02220.0514-0.02340.1319-0.07230.0807-0.07530.00970.1489-0.009-0.00090.1639-0.06880.0787-9.2188-28.0603-8.4507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 266
2X-RAY DIFFRACTION2B94 - 266
3X-RAY DIFFRACTION3A301 - 304
4X-RAY DIFFRACTION4B301 - 304

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