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- PDB-3trp: Crystal structure of recombinant rabbit skeletal calsequestrin -

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Basic information

Entry
Database: PDB / ID: 3trp
TitleCrystal structure of recombinant rabbit skeletal calsequestrin
ComponentsCalsequestrin-1
KeywordsCalcium-binding protein
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.8817 Å
AuthorsSanchez, E.J. / Lewis, K.M. / Munske, G.R. / Nissen, M.S. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: High-capacity Ca2+ Binding of Human Skeletal Calsequestrin.
Authors: Sanchez, E.J. / Lewis, K.M. / Danna, B.R. / Kang, C.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_site
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_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,58813
Polymers40,8291
Non-polymers75912
Water7,855436
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)83,17626
Polymers81,6582
Non-polymers1,51824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area8580 Å2
ΔGint-215 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.122, 144.863, 110.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40828.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CASQ1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07221

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Non-polymers , 5 types, 448 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


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


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


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


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.92 Å3/Da / Density % sol: 57.82 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 8.2.11
SYNCHROTRONALS 8.2.22
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
ADSC QUANTUM 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.88→38.864 Å / Num. obs: 37750

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1A8Y

1a8y


Resolution: 1.8817→38.864 Å / SU ML: 0.21 / σ(F): 0.19 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 1938 5.13 %
Rwork0.1781 --
obs0.1796 37750 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.565 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5577 Å20 Å20 Å2
2--0.3817 Å20 Å2
3---3.176 Å2
Refinement stepCycle: LAST / Resolution: 1.8817→38.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 40 436 3341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133020
X-RAY DIFFRACTIONf_angle_d0.9354107
X-RAY DIFFRACTIONf_dihedral_angle_d12.9011125
X-RAY DIFFRACTIONf_chiral_restr0.067442
X-RAY DIFFRACTIONf_plane_restr0.004540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8817-1.92880.27041160.22532236X-RAY DIFFRACTION86
1.9288-1.98090.24781310.19922442X-RAY DIFFRACTION94
1.9809-2.03920.23931340.19062498X-RAY DIFFRACTION96
2.0392-2.1050.22711370.18892503X-RAY DIFFRACTION96
2.105-2.18020.23721390.17992539X-RAY DIFFRACTION97
2.1802-2.26750.24621360.18762518X-RAY DIFFRACTION97
2.2675-2.37070.23781410.19182590X-RAY DIFFRACTION98
2.3707-2.49570.2471380.18982565X-RAY DIFFRACTION99
2.4957-2.6520.22861410.18772591X-RAY DIFFRACTION99
2.652-2.85670.23871410.20032615X-RAY DIFFRACTION99
2.8567-3.14410.23211440.18752629X-RAY DIFFRACTION99
3.1441-3.59880.16251430.16332628X-RAY DIFFRACTION100
3.5988-4.5330.15441460.14342683X-RAY DIFFRACTION100
4.533-38.87230.18551510.16832775X-RAY DIFFRACTION99

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