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

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Basic information

Entry
Database: PDB / ID: 4phj
TitleThe Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids: Human unliganded protein
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / Domain VI / PEF(S) / Calcium Binding / Protease
Function / homology
Function and homology information


calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome ...calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / membrane / plasma membrane / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAdams, S.E. / Rizkallah, P.J. / Allemann, R.K. / Miller, D.J. / Hallett, M.B. / Robinson, E.
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 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_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.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)40,35410
Polymers40,0332
Non-polymers3218
Water6,774376
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-122 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.630, 79.310, 57.100
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A94 - 266
2010B94 - 266

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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: 20016.607 Da / Num. of mol.: 2 / Fragment: Penta EF-hands subunit, Residues 96-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Production host: Escherichia coli (E. coli) / References: UniProt: P04632
#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.: 376 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
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
Temp details: Steady temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→49.61 Å / Num. all: 51828 / Num. obs: 51828 / % possible obs: 89 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.3 / % possible all: 83.8

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Processing

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

1alv


Resolution: 1.6→49.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19959 2638 5.1 %RANDOM
Rwork0.16622 ---
obs0.16794 49153 88.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0.58 Å2
2--0.11 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.6→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 8 376 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193149
X-RAY DIFFRACTIONr_bond_other_d00.022915
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9364277
X-RAY DIFFRACTIONr_angle_other_deg3.73836715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0985404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72223.916166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31815577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521527
X-RAY DIFFRACTIONr_chiral_restr0.130.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023755
X-RAY DIFFRACTIONr_gen_planes_other0.0250.02804
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_it1.71.6871534
X-RAY DIFFRACTIONr_mcbond_other1.6921.6861533
X-RAY DIFFRACTIONr_mcangle_it2.4372.5211959
X-RAY DIFFRACTIONr_mcangle_other2.4362.5221960
X-RAY DIFFRACTIONr_scbond_it2.7322.0121615
X-RAY DIFFRACTIONr_scbond_other2.7272.0121614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1062.9052315
X-RAY DIFFRACTIONr_long_range_B_refined6.88815.6314227
X-RAY DIFFRACTIONr_long_range_B_other6.66914.6293993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20183 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 174 -
Rwork0.257 3413 -
obs--83.67 %
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)
11.67512.65114.01124.54346.04049.92830.0763-0.01970.05370.0966-0.13440.16580.16390.080.0580.0675-0.00840.02860.0841-0.00270.0567-5.43-3.709-12.249
20.68020.32560.12710.46120.10650.54570.0706-0.0924-0.04210.1514-0.0430.08640.1242-0.036-0.02760.0928-0.00760.02040.0703-0.01150.0515-10.604-0.295-13.233
30.3758-0.0386-0.30361.1833-0.20090.29090.06130.0063-0.0429-0.022-0.09150.0217-0.04680.01250.03020.03520.0055-0.00830.0305-0.00340.02265.4713.595-29.056
40.79430.0759-0.02830.87770.35880.33840.010.02370.0408-0.07280.0287-0.033-0.06720.0369-0.03880.0166-0.0070.00590.0070.00020.01384.2999.978-28.443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A301 - 304
2X-RAY DIFFRACTION2A96 - 266
3X-RAY DIFFRACTION3B301 - 304
4X-RAY DIFFRACTION4B96 - 266

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