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- PDB-6o6j: Crystal structure of the LjCASTOR gating ring in the Ca2+ and Na+... -

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Basic information

Entry
Database: PDB / ID: 6o6j
TitleCrystal structure of the LjCASTOR gating ring in the Ca2+ and Na+ condition
ComponentsIon channel CASTOR
KeywordsTRANSPORT PROTEIN / calcium channel / RCK domain / gating ring / CASTOR / membrane protein
Function / homologyCASTOR/POLLUX/SYM8 ion channel, conserved domain / Ion channel CASTOR/POLLUX/SYM8-like / Castor and Pollux, part of voltage-gated ion channel / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / monoatomic ion transmembrane transport / nuclear membrane / Ion channel CASTOR
Function and homology information
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJiang, Y. / Kim, S.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Y.J. United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
CitationJournal: Nat Commun / Year: 2019
Title: Ca2+-regulated Ca2+channels with an RCK gating ring control plant symbiotic associations.
Authors: Kim, S. / Zeng, W. / Bernard, S. / Liao, J. / Venkateshwaran, M. / Ane, J.M. / Jiang, Y.
History
DepositionMar 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion channel CASTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1477
Polymers61,9571
Non-polymers1916
Water9,620534
1
A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,59028
Polymers247,8274
Non-polymers76224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9530 Å2
ΔGint-279 kcal/mol
Surface area81270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.234, 125.234, 81.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Ion channel CASTOR


Mass: 61956.867 Da / Num. of mol.: 1 / Fragment: gating ring (UNP residues 312-853)
Source method: isolated from a genetically manipulated source
Details: Jean-Michel Ane, University of Wisconsin - Madison, Madison, WI 53706, USA.
Source: (gene. exp.) Lotus japonicus (plant) / Gene: CASTOR / Variant: Gifu / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q5H8A6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.83 Å3/Da / Density % sol: 56.47 % / Description: a thin rectangular prism with smooth edges
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 21% w/v PEG550 MME, 50 mM magnesium acetate, 100 mM Tris, pH 8.2
PH range: 7.5-8.5 / Temp details: 293 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94936 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 160841 / % possible obs: 98.75 % / Redundancy: 5 % / Biso Wilson estimate: 17.93 Å2 / Net I/σ(I): 34.54
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.983 / Num. unique obs: 7449 / CC1/2: 0.405 / Rpim(I) all: 0.671 / Rrim(I) all: 1.382 / Rsym value: 1.201 / Χ2: 1.149 / % possible all: 90.21

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASER1.13_2998phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→39.6 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4919
RfactorNum. reflection% reflection
Rfree0.1882 3823 2.47 %
Rwork0.1659 --
obs0.1665 154888 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 6 534 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014045
X-RAY DIFFRACTIONf_angle_d1.06485474
X-RAY DIFFRACTIONf_chiral_restr0.0719635
X-RAY DIFFRACTIONf_plane_restr0.0066712
X-RAY DIFFRACTIONf_dihedral_angle_d10.99542513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27051060.26734396X-RAY DIFFRACTION74.66
1.62-1.640.23091150.25644833X-RAY DIFFRACTION82.45
1.64-1.670.29191470.24645304X-RAY DIFFRACTION90.9
1.67-1.690.20431440.23165607X-RAY DIFFRACTION95.96
1.69-1.720.22731480.2265711X-RAY DIFFRACTION95.95
1.72-1.740.24621430.21785627X-RAY DIFFRACTION95.94
1.74-1.770.24531420.22875643X-RAY DIFFRACTION95.95
1.77-1.80.26531420.21095616X-RAY DIFFRACTION96.4
1.8-1.830.21571480.2055654X-RAY DIFFRACTION96.3
1.83-1.870.22581430.18485706X-RAY DIFFRACTION96.45
1.87-1.910.17411480.1735658X-RAY DIFFRACTION96.51
1.91-1.950.23131440.17825631X-RAY DIFFRACTION96.56
1.95-20.21241410.17145676X-RAY DIFFRACTION96.66
2-2.040.19181460.16955667X-RAY DIFFRACTION97.05
2.04-2.10.19851460.16365708X-RAY DIFFRACTION96.98
2.1-2.160.15541520.16375739X-RAY DIFFRACTION97.36
2.16-2.230.21861500.15945648X-RAY DIFFRACTION97.17
2.23-2.310.17771450.15445750X-RAY DIFFRACTION97.12
2.31-2.40.16631340.15975703X-RAY DIFFRACTION97.43
2.4-2.510.19931430.1555784X-RAY DIFFRACTION97.82
2.51-2.650.17151450.16195752X-RAY DIFFRACTION97.78
2.65-2.810.19931410.16145717X-RAY DIFFRACTION97.91
2.81-3.030.21051450.16895756X-RAY DIFFRACTION97.96
3.03-3.330.21621430.16195745X-RAY DIFFRACTION98.05
3.33-3.820.16291370.14675794X-RAY DIFFRACTION98.18
3.82-4.810.1361440.13085784X-RAY DIFFRACTION98.18
4.81-39.610.16641410.16255456X-RAY DIFFRACTION92.94

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