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- PDB-6iz6: Crystal Structure Analysis of TRIC counter-ion channels in calciu... -

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Basic information

Entry
Database: PDB / ID: 6iz6
TitleCrystal Structure Analysis of TRIC counter-ion channels in calcium release
ComponentsTrimeric intracellular cation channel type B-B
KeywordsMEMBRANE PROTEIN / TRIC / cation channel
Function / homologyTRIC channel / TRIC channel / regulation of release of sequestered calcium ion into cytosol / potassium channel activity / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / Trimeric intracellular cation channel type B-B
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.293 Å
AuthorsLiu, X.L. / Wang, X.H. / Su, M. / Hendrickson, W.A. / Chen, Y.H.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500503 China
Ministry of Science and Technology (China)2015CB910102 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis for activity of TRIC counter-ion channels in calcium release.
Authors: Wang, X.H. / Su, M. / Gao, F. / Xie, W. / Zeng, Y. / Li, D.L. / Liu, X.L. / Zhao, H. / Qin, L. / Li, F. / Liu, Q. / Clarke, O.B. / Lam, S.M. / Shui, G.H. / Hendrickson, W.A. / Chen, Y.H.
History
DepositionDec 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimeric intracellular cation channel type B-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5042
Polymers35,4641
Non-polymers401
Water362
1
A: Trimeric intracellular cation channel type B-B
hetero molecules

A: Trimeric intracellular cation channel type B-B
hetero molecules

A: Trimeric intracellular cation channel type B-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5126
Polymers106,3923
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
Buried area4970 Å2
ΔGint-62 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.110, 250.110, 250.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21A-502-

HOH

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Components

#1: Protein Trimeric intracellular cation channel type B-B / TRICB-B / Transmembrane protein 38B-B


Mass: 35463.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: tmem38b-b / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q6GN30
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.6 Å3/Da / Density % sol: 73.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG 350 MME, CaCl2, MES PH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3.29→48.134 Å / Num. obs: 9924 / % possible obs: 92.6 % / Redundancy: 82.8 % / CC1/2: 1 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.023 / Rrim(I) all: 0.214 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.29-3.5544.26.96618120.5831.0437.04784.7
8.71-48.1392.70.08867910.0090.08899.4

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IZ5

6iz5


Resolution: 3.293→48.134 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 53.15
RfactorNum. reflection% reflection
Rfree0.3542 456 4.66 %
Rwork0.3263 --
obs0.3276 9779 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 267.33 Å2 / Biso mean: 149.6937 Å2 / Biso min: 66.98 Å2
Refinement stepCycle: final / Resolution: 3.293→48.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 1 2 1769
Biso mean--182.68 95.28 -
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2932-3.76960.46321410.45612621276280
3.7696-4.74860.35651460.31793137328394
4.7486-48.13880.34111690.315935653734100

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