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- PDB-8f48: Human CASQ1 mutant - S248E -

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Basic information

Entry
Database: PDB / ID: 8f48
TitleHuman CASQ1 mutant - S248E
ComponentsCalsequestrin-1
KeywordsMETAL BINDING PROTEIN / calcium binding protein
Function / homology
Function and homology information


terminal cisterna lumen / 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 / response to denervation involved in regulation of muscle adaptation / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / smooth endoplasmic reticulum ...terminal cisterna lumen / 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 / response to denervation involved in regulation of muscle adaptation / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / smooth endoplasmic reticulum / skeletal muscle tissue development / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / : / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / 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. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMayfield, J.E. / Dixon, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK018849-44 United States
CitationJournal: To Be Published
Title: Human CASQ1 mutant - S248E
Authors: Mayfield, J.E. / Dixon, J.E.
History
DepositionNov 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calsequestrin-1
B: Calsequestrin-1


Theoretical massNumber of molelcules
Total (without water)84,2402
Polymers84,2402
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-31 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 107.340, 108.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 42119.965 Da / Num. of mol.: 2 / Mutation: S248E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1 / Details: 0.1M sodium acetate, 8% PEG 400, pH 4.1

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.9→48.3 Å / Num. obs: 16929 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 51.28 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 9.39
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 1637 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CRD

5crd


Resolution: 2.9→48.3 Å / SU ML: 0.3363 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.3585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2885 1679 9.92 %
Rwork0.2178 15250 -
obs0.2248 16929 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 0 13 5513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225625
X-RAY DIFFRACTIONf_angle_d0.48847632
X-RAY DIFFRACTIONf_chiral_restr0.0437827
X-RAY DIFFRACTIONf_plane_restr0.00311011
X-RAY DIFFRACTIONf_dihedral_angle_d4.7256706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.35551290.27551223X-RAY DIFFRACTION98.33
2.99-3.080.32171330.26061226X-RAY DIFFRACTION98.26
3.08-3.190.34041410.26441252X-RAY DIFFRACTION99.08
3.19-3.320.34071380.27471239X-RAY DIFFRACTION99.57
3.32-3.470.32571440.24261266X-RAY DIFFRACTION99.79
3.47-3.650.34141350.22521252X-RAY DIFFRACTION100
3.65-3.880.29641390.22841275X-RAY DIFFRACTION99.93
3.88-4.180.2951400.21431268X-RAY DIFFRACTION100
4.18-4.60.23111430.181285X-RAY DIFFRACTION99.86
4.6-5.270.27031430.18531272X-RAY DIFFRACTION99.93
5.27-6.630.3011440.21641315X-RAY DIFFRACTION99.86
6.63-48.30.22611500.19461377X-RAY DIFFRACTION99.87

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