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- PDB-5crg: Human skeletal calsequestrin, D210G mutant high-calcium complex -

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Basic information

Entry
Database: PDB / ID: 5crg
TitleHuman skeletal calsequestrin, D210G mutant high-calcium complex
ComponentsCalsequestrin-1
KeywordsCalcium 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. / 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: 1.97 Å
AuthorsLewis, K.M. / Ronish, L.A. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM11125401 United States
M.J. Murdock Charitable Trust United States
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 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calsequestrin-1
B: Calsequestrin-1
C: Calsequestrin-1
D: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,94586
Polymers166,6584
Non-polymers3,28682
Water46,0102554
1
A: Calsequestrin-1
B: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,97243
Polymers83,3292
Non-polymers1,64341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Calsequestrin-1
D: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,97243
Polymers83,3292
Non-polymers1,64341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.179, 67.462, 158.062
Angle α, β, γ (deg.)90.00, 96.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41664.543 Da / Num. of mol.: 4 / Fragment: residues 35-396 / Mutation: D210G
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.: 82 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2554 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
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: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→45.298 Å / Num. obs: 129904 / % possible obs: 96.06 % / Redundancy: 3.4 % / Net I/σ(I): 10
Reflection shellNum. unique all: 9206

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Processing

Software
NameVersionClassification
PHENIX(1.10-2152_1692: ???)refinement
HKL-2000data reduction
Coot8.1model building
PHENIX1.9-1692phasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CRD

5crd


Resolution: 1.97→45.298 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1931 1752 1.35 %
Rwork0.1754 --
obs0.1756 129904 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→45.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11413 0 82 2554 14049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211687
X-RAY DIFFRACTIONf_angle_d0.49315880
X-RAY DIFFRACTIONf_dihedral_angle_d19.4687029
X-RAY DIFFRACTIONf_chiral_restr0.0441722
X-RAY DIFFRACTIONf_plane_restr0.0032121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.02330.28341260.22799206X-RAY DIFFRACTION90
2.0233-2.08280.23221270.20789318X-RAY DIFFRACTION92
2.0828-2.150.23031280.19569385X-RAY DIFFRACTION92
2.15-2.22690.23911310.18919583X-RAY DIFFRACTION93
2.2269-2.3160.24291310.19249598X-RAY DIFFRACTION94
2.316-2.42140.20881340.18539779X-RAY DIFFRACTION96
2.4214-2.54910.20441340.18599840X-RAY DIFFRACTION97
2.5491-2.70880.21861390.186410077X-RAY DIFFRACTION98
2.7088-2.91790.1851380.180910106X-RAY DIFFRACTION99
2.9179-3.21150.18481380.17510189X-RAY DIFFRACTION99
3.2115-3.6760.18231400.155910229X-RAY DIFFRACTION99
3.676-4.63060.15391410.143410328X-RAY DIFFRACTION100
4.6306-45.30980.16151450.170510514X-RAY DIFFRACTION100

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