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- PDB-3v1w: Molecular Basis for Multiple Ligand Binding of Calsequestrin and ... -

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Basic information

Entry
Database: PDB / ID: 3v1w
TitleMolecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin
ComponentsCalsequestrin-1
KeywordsCALCIUM BINDING PROTEIN / Thioredoxin fold
Function / homology
Function and homology information


positive regulation of store-operated calcium channel activity / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / ion binding / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol ...positive regulation of store-operated calcium channel activity / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / ion binding / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Z disc / mitochondrial matrix / calcium ion binding / magnesium ion binding / protein homodimerization activity / metal ion binding
Similarity search - Function
Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin ...Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.908 Å
AuthorsSubramanian, A.K. / Nissen, M.N. / Lewis, K.M. / Sanchez, E.J. / Muralidharan, A.K. / Kang, C.
CitationJournal: To be Published
Title: Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin
Authors: Subramanian, A.K. / Nissen, M.N. / Lewis, K.M. / Sanchez, E.J. / Muralidharan, A.K. / Kang, C.
History
DepositionDec 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,45311
Polymers42,4681
Non-polymers98510
Water9,260514
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calsequestrin-1
hetero molecules

A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,90722
Polymers84,9362
Non-polymers1,97020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area9120 Å2
ΔGint-195 kcal/mol
Surface area34060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.082, 144.592, 110.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Calsequestrin-1 / Aspartactin / Calsequestrin / skeletal muscle isoform / Laminin-binding protein


Mass: 42468.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P07221
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 523 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.79 Å3/Da / Density % sol: 55.92 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.908→44.0149 Å / Num. obs: 36850

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TRQ

3trq


Resolution: 1.908→38.95 Å / SU ML: 0.24 / σ(F): 0.16 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1981 5.38 %
Rwork0.1709 --
obs0.1736 36846 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.825 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9985 Å20 Å20 Å2
2--1.3285 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 1.908→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 58 514 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143018
X-RAY DIFFRACTIONf_angle_d1.1224139
X-RAY DIFFRACTIONf_dihedral_angle_d16.3111128
X-RAY DIFFRACTIONf_chiral_restr0.082443
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.908-1.95570.25291310.17952284X-RAY DIFFRACTION92
1.9557-2.00860.22911380.1842442X-RAY DIFFRACTION98
2.0086-2.06770.27211390.16952443X-RAY DIFFRACTION98
2.0677-2.13450.23881400.1732465X-RAY DIFFRACTION99
2.1345-2.21070.25791390.16732465X-RAY DIFFRACTION98
2.2107-2.29920.23921400.17992469X-RAY DIFFRACTION99
2.2992-2.40390.23061410.17072464X-RAY DIFFRACTION99
2.4039-2.53060.24921420.1872506X-RAY DIFFRACTION99
2.5306-2.68910.24621420.18322509X-RAY DIFFRACTION99
2.6891-2.89670.26141420.1882512X-RAY DIFFRACTION100
2.8967-3.1880.19531440.18052531X-RAY DIFFRACTION100
3.188-3.64910.20241450.15172530X-RAY DIFFRACTION100
3.6491-4.59630.17731450.14692574X-RAY DIFFRACTION100
4.5963-38.95780.22571530.17272671X-RAY DIFFRACTION99

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