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- PDB-2vaf: Crystal structure of Human Cardiac Calsequestrin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2vaf
TitleCrystal structure of Human Cardiac Calsequestrin
ComponentsCALSEQUESTRIN-2
KeywordsMETAL BINDING PROTEIN / CALCIUM / GLYCOPROTEIN / POLYMORPHISM / MUSCLE PROTEIN / DISEASE MUTATION / SARCOPLASMIC RETICULUM / CRYSTAL STRUCTURE HUMAN CARDIAC CALSEQUESTRIN / METAL-BINDING PROTEIN
Function / homology
Function and homology information


calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / sequestering of calcium ion / junctional sarcoplasmic reticulum membrane / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / ion binding / cellular response to caffeine ...calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / sequestering of calcium ion / junctional sarcoplasmic reticulum membrane / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / ion binding / cellular response to caffeine / negative regulation of potassium ion transport / protein polymerization / detection of calcium ion / striated muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of heart rate / sarcoplasmic reticulum / intracellular calcium ion homeostasis / Stimuli-sensing channels / Z disc / calcium-dependent protein binding / calcium ion binding / protein homodimerization activity / cytoplasm
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsKim, E. / Youn, B. / Kemper, L. / Campbell, C. / Milting, H. / Varsanyi, M. / Kang, C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Characterization of Human Cardiac Calsequestrin and its Deleterious Mutants.
Authors: Kim, E. / Youn, B. / Kemper, L. / Campbell, C. / Milting, H. / Varsanyi, M. / Kang, C.
History
DepositionAug 31, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionSep 11, 2007ID: 2V0Q
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-2


Theoretical massNumber of molelcules
Total (without water)43,9981
Polymers43,9981
Non-polymers00
Water0
1
A: CALSEQUESTRIN-2

A: CALSEQUESTRIN-2


Theoretical massNumber of molelcules
Total (without water)87,9952
Polymers87,9952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area4860 Å2
ΔGint-28.8 kcal/mol
Surface area43450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)150.650, 150.650, 227.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CALSEQUESTRIN-2 / / CALSEQUESTRIN / CARDIAC MUSCLE ISOFORM / HUMAN CARDIAC CALSEQUESTRIN


Mass: 43997.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14958

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 8.02 Å3/Da / Density % sol: 84.55 % / Description: NONE

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07812
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 11522 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.56

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Processing

Software
NameClassification
X-PLORrefinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJI

1sji


Resolution: 3.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.325 -5 %
Rwork0.274 --
obs0.274 4119 88.7 %
Refinement stepCycle: LAST / Resolution: 3.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 0 0 2873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.986
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 fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO

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