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- PDB-1alw: INHIBITOR AND CALCIUM BOUND DOMAIN VI OF PORCINE CALPAIN -

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Basic information

Entry
Database: PDB / ID: 1alw
TitleINHIBITOR AND CALCIUM BOUND DOMAIN VI OF PORCINE CALPAIN
ComponentsCALPAIN
KeywordsCALCIUM BINDING / CALMODULIN LIKE / DOMAIN OF CYSTEIN PROTEASE
Function / homology
Function and homology information


Degradation of the extracellular matrix / Formation of the cornified envelope / 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
3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID / Calpain small subunit 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsNarayana, S.V.L. / Lin, G.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of calcium bound domain VI of calpain at 1.9 A resolution and its role in enzyme assembly, regulation, and inhibitor binding.
Authors: Lin, G.D. / Chattopadhyay, D. / Maki, M. / Wang, K.K. / Carson, M. / Jin, L. / Yuen, P.W. / Takano, E. / Hatanaka, M. / DeLucas, L.J. / Narayana, S.V.
History
DepositionJun 4, 1997Processing site: BNL
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 7, 2024Group: 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_struct_conn_angle / software / struct_conn / 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_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 / _software.name / _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.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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALPAIN
B: CALPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,70412
Polymers39,7672
Non-polymers93710
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-120 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.870, 80.460, 57.080
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3834, 0.923124, 0.029108), (0.923568, 0.383382, 0.006414), (-0.005238, 0.029342, -0.999556)
Vector: 33.14851, -23.37659, 99.84097)

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Components

#1: Protein CALPAIN / / S-CAMLD


Mass: 19883.477 Da / Num. of mol.: 2 / Fragment: INHIBITOR-BOUND CALCIUM BINDING DOMAIN VI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / 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: Chemical ChemComp-ISA / 3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID / PD150606


Mass: 308.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9IO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG6000 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: PEG6000

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→20 Å / Num. obs: 24588 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.08 / Net I/σ(I): 4.5
Reflection shellResolution: 2.03→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.26 / % possible all: 90
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.5refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S-CAMLD

Resolution: 2.03→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -10 %RANDOM
Rwork0.21 ---
obs0.21 33809 97 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.03→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 34 104 2928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.494
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1TOPH19X.PRO
X-RAY DIFFRACTION2CAPDAWT.TOPCAPDAWT.PAR
X-RAY DIFFRACTION3TOPHCSDX.PROPARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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