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- PDB-5kn2: Native bovine skeletal calsequestrin, high-Ca2+ form -

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Basic information

Entry
Database: PDB / ID: 5kn2
TitleNative bovine skeletal calsequestrin, high-Ca2+ form
ComponentsCalsequestrin
KeywordsMETAL BINDING PROTEIN / calsequestrin / calcium / polymerization / glycosylation
Function / homology
Function and homology information


Stimuli-sensing channels / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / Ion homeostasis / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol ...Stimuli-sensing channels / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / Ion homeostasis / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / Z disc / response to heat / mitochondrial matrix / calcium ion binding / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsLewis, K.M. / Byrd, S.S. / 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: Int J Mol Sci / Year: 2016
Title: Characterization of Post-Translational Modifications to Calsequestrins of Cardiac and Skeletal Muscle.
Authors: Lewis, K.M. / Munske, G.R. / Byrd, S.S. / Kang, J. / Cho, H.J. / Rios, E. / Kang, C.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: Calsequestrin
C: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,49945
Polymers124,6633
Non-polymers2,83642
Water905
1
A: Calsequestrin
hetero molecules

A: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,99930
Polymers83,1092
Non-polymers1,89128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8150 Å2
ΔGint-290 kcal/mol
Surface area32970 Å2
MethodPISA
2
B: Calsequestrin
C: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,99930
Polymers83,1092
Non-polymers1,89128
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-293 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.363, 169.194, 155.477
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-505-

HOH

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Components

#1: Protein Calsequestrin


Mass: 41554.277 Da / Num. of mol.: 3 / Fragment: UNP residues 35-395 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q05JF3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 27.5 % 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 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.601→49.957 Å / Num. obs: 52807 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.0633 / Net I/σ(I): 13.25
Reflection shellResolution: 2.601→2.674 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 2.17 / Num. measured obs: 5112 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000v712data reduction
HKL-2000v712data scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KN1

5kn1


Resolution: 2.601→49.947 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.51
RfactorNum. reflection% reflection
Rfree0.2411 1998 3.78 %
Rwork0.2053 --
obs0.2066 52795 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.601→49.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8540 0 39 5 8584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058741
X-RAY DIFFRACTIONf_angle_d0.84311908
X-RAY DIFFRACTIONf_dihedral_angle_d17.0465224
X-RAY DIFFRACTIONf_chiral_restr0.0531312
X-RAY DIFFRACTIONf_plane_restr0.0051585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6013-2.66630.35011360.33643469X-RAY DIFFRACTION96
2.6663-2.73840.35171420.30853611X-RAY DIFFRACTION100
2.7384-2.8190.32731400.29993585X-RAY DIFFRACTION100
2.819-2.910.31751430.28883595X-RAY DIFFRACTION100
2.91-3.01390.33361420.29053608X-RAY DIFFRACTION100
3.0139-3.13460.35831420.27573617X-RAY DIFFRACTION100
3.1346-3.27720.36681430.25643624X-RAY DIFFRACTION100
3.2772-3.450.26131420.23073623X-RAY DIFFRACTION100
3.45-3.66610.2591430.2063625X-RAY DIFFRACTION100
3.6661-3.9490.24081420.19253647X-RAY DIFFRACTION100
3.949-4.34620.22231440.17043635X-RAY DIFFRACTION100
4.3462-4.97460.21251440.15113672X-RAY DIFFRACTION100
4.9746-6.26560.22361460.20173701X-RAY DIFFRACTION100
6.2656-49.95660.19931490.19673785X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61941.23220.67291.7848-0.55562.31260.0285-0.0706-0.0370.0053-0.172-0.1814-0.25260.69210.00010.7183-0.1434-0.02930.9367-0.07540.6818154.990514.75097.0403
22.7317-0.68210.44171.6541-1.11261.7592-0.0675-0.23340.34380.1940.25270.3417-0.2477-0.1825-0.00010.69460.0840.06430.5441-0.03970.5485124.709918.424210.5052
30.98540.854-0.41521.3074-0.13981.2749-0.00180.1141-0.09590.09740.0856-0.02670.01460.166700.68340.0972-0.05760.6356-0.01020.5115134.5204-7.867817.3926
41.016-0.45651.07890.1342-0.41761.08740.0730.4544-0.5280.04050.1565-0.26720.61330.02850.00021.0609-0.20370.07571.2936-0.38151.0747158.48447.091643.0531
51.05970.97510.37071.8166-0.80053.2918-0.37960.6904-0.4601-0.12880.2768-0.04790.3339-0.2651-0.00070.9885-0.32170.02191.1453-0.18770.847156.83815.269941.6445
61.7473-0.11060.23790.4678-0.30280.9321-0.19491.05091.3122-0.1951-0.00710.1538-0.1107-0.0647-0.00030.8845-0.2141-0.21011.10860.21931.1878146.640739.180745.2294
71.69570.26660.64052.1923-0.88590.858-0.43651.29171.828-0.5399-0.08820.1632-0.63070.2327-0.00381.2538-0.3304-0.35481.58240.44721.4818148.430943.778636.5037
80.05750.21410.33910.80940.77530.9701-0.34951.2540.03010.10070.3980.5322-0.09890.09340.00260.9399-0.4614-0.04191.65620.15340.8944169.482237.763735.3414
90.25480.0256-0.21950.107-0.00610.34370.25231.01560.6471-0.40250.5589-1.2988-0.09250.45830.00091.3641-0.38020.1832.00690.08211.3118180.666132.723431.6056
100.33030.03560.08820.60750.10390.03470.069-0.270.2005-1.09950.4289-1.2791-0.8221.18280.00441.7249-0.3912-0.012.1970.17111.5452178.066246.210826.8669
111.9551.28180.2374.0570.31281.3417-0.18140.3058-0.02620.1990.088-0.9314-0.17230.463800.7236-0.1576-0.16280.8737-0.01051.1365185.259532.520257.7297
123.88050.8883-1.01940.29680.12131.32980.01490.1790.15660.0241-0.0307-0.2902-0.12310.41990.00010.8059-0.174-0.21280.56410.02670.7561164.563933.555964.6894
132.53461.0517-0.42950.77250.22640.38430.4458-0.31610.1994-0.2276-0.19160.47060.4219-0.4884-0.00010.9075-0.1285-0.01610.6757-0.02380.8918154.740932.251871.4965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:129)
2X-RAY DIFFRACTION2(chain A and resid 130:227)
3X-RAY DIFFRACTION3(chain A and resid 228:355)
4X-RAY DIFFRACTION4(chain B and resid 4:50)
5X-RAY DIFFRACTION5(chain B and resid 51:126)
6X-RAY DIFFRACTION6(chain B and resid 127:180)
7X-RAY DIFFRACTION7(chain B and resid 181:232)
8X-RAY DIFFRACTION8(chain B and resid 233:294)
9X-RAY DIFFRACTION9(chain B and resid 295:326)
10X-RAY DIFFRACTION10(chain B and resid 327:354)
11X-RAY DIFFRACTION11(chain C and resid 3:227)
12X-RAY DIFFRACTION12(chain C and resid 228:301)
13X-RAY DIFFRACTION13(chain C and resid 302:354)

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