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- PDB-5crd: Wild-type human skeletal calsequestrin -

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Basic information

Entry
Database: PDB / ID: 5crd
TitleWild-type human skeletal calsequestrin
ComponentsCalsequestrin-1
KeywordsCalcium Binding Protein
Function / homology
Function and homology information


terminal cisterna lumen / positive regulation of store-operated calcium channel activity / response to denervation involved in regulation of muscle adaptation / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / endoplasmic reticulum organization / sarcomere organization / smooth endoplasmic reticulum / protein polymerization ...terminal cisterna lumen / positive regulation of store-operated calcium channel activity / response to denervation involved in regulation of muscle adaptation / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / endoplasmic reticulum organization / sarcomere organization / smooth endoplasmic reticulum / protein polymerization / skeletal muscle tissue development / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / positive regulation of release of sequestered calcium ion into cytosol / Stimuli-sensing channels / Z disc / response to heat / mitochondrial matrix / calcium ion binding / endoplasmic reticulum / mitochondrion / identical protein 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLewis, K.M. / Ronish, L.A. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterization of Two Human Skeletal Calsequestrin Mutants Implicated in Malignant Hyperthermia and Vacuolar Aggregate Myopathy.
Authors: Lewis, K.M. / Ronish, L.A. / Rios, E. / Kang, C.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1197
Polymers41,7231
Non-polymers3976
Water4,197233
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)84,23814
Polymers83,4452
Non-polymers79312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6900 Å2
ΔGint-169 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.170, 145.132, 110.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Calsequestrin-1 / Calmitine / Calsequestrin / skeletal muscle isoform


Mass: 41722.578 Da / Num. of mol.: 1 / Fragment: residues 35-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ1, CASQ / Production host: Escherichia coli (E. coli) / References: UniProt: P31415
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MOPS, 27.5 % (v/v) 2-methyl-2,4-pentanediol, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→43.894 Å / Num. obs: 28782 / % possible obs: 99.37 % / Redundancy: 6.8 % / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIX1.10-2152_1692refinement
HKL-2000data reduction
Coot8.1model building
PHENIX1.9-1692phasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TRQ

3trq


Resolution: 2.08→43.894 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1560 5.42 %
Rwork0.1893 --
obs0.1908 28775 99.37 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→43.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 20 233 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072922
X-RAY DIFFRACTIONf_angle_d0.5033960
X-RAY DIFFRACTIONf_dihedral_angle_d15.0811748
X-RAY DIFFRACTIONf_chiral_restr0.043429
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.14720.26951390.24322421X-RAY DIFFRACTION99
2.1472-2.22390.26541390.24542427X-RAY DIFFRACTION99
2.2239-2.31290.30221410.24522450X-RAY DIFFRACTION99
2.3129-2.41820.26071390.2232436X-RAY DIFFRACTION99
2.4182-2.54570.28181410.22812455X-RAY DIFFRACTION99
2.5457-2.70510.25751410.20962457X-RAY DIFFRACTION99
2.7051-2.9140.26891390.21192437X-RAY DIFFRACTION99
2.914-3.20710.21171420.19642470X-RAY DIFFRACTION100
3.2071-3.6710.20161440.17532516X-RAY DIFFRACTION100
3.671-4.62430.17721450.14722524X-RAY DIFFRACTION100
4.6243-43.90350.18061500.17412622X-RAY DIFFRACTION100

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