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- PDB-5h36: Crystal structures of the TRIC trimeric intracellular cation chan... -

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Basic information

Entry
Database: PDB / ID: 5h36
TitleCrystal structures of the TRIC trimeric intracellular cation channel orthologue from Rhodobacter sphaeroides
ComponentsUncharacterized protein TRIC
KeywordsMEMBRANE PROTEIN / ion channels
Function / homologyGlycine transporter / Glycine transporter / plasma membrane / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Glycine transporter domain-containing protein
Function and homology information
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.409 Å
AuthorsKasuya, G. / Hiraizumi, M. / Hattori, M. / Nureki, O.
CitationJournal: Cell Res. / Year: 2016
Title: Crystal structures of the TRIC trimeric intracellular cation channel orthologues
Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / ...Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / Takemoto, M. / Kato, H.E. / Yamashita, K. / Wada, M. / Ito, K. / Ishitani, R. / Hattori, M. / Nureki, O.
History
DepositionOct 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
E: Uncharacterized protein TRIC
A: Uncharacterized protein TRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9254
Polymers45,5672
Non-polymers1,3582
Water00
1
E: Uncharacterized protein TRIC
hetero molecules

E: Uncharacterized protein TRIC
hetero molecules

E: Uncharacterized protein TRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3886
Polymers68,3513
Non-polymers2,0373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7550 Å2
ΔGint-76 kcal/mol
Surface area21290 Å2
MethodPISA
2
A: Uncharacterized protein TRIC
hetero molecules

A: Uncharacterized protein TRIC
hetero molecules

A: Uncharacterized protein TRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3886
Polymers68,3513
Non-polymers2,0373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7690 Å2
ΔGint-76 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.010, 156.010, 82.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Uncharacterized protein TRIC


Mass: 22783.598 Da / Num. of mol.: 2 / Fragment: UNP residues 1-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_3856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HKN0
#2: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM

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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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 25-32% (v/v) PEG 400, 20-70mM Li2SO4, 20-70mM Na2SO4, 50mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.409→50 Å / Num. obs: 9730 / % possible obs: 95.3 % / Redundancy: 5.1 % / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3.409→45.036 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.53
RfactorNum. reflection% reflection
Rfree0.2732 967 9.94 %
Rwork0.2471 --
obs0.2627 9730 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.409→45.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 28 0 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042880
X-RAY DIFFRACTIONf_angle_d0.963919
X-RAY DIFFRACTIONf_dihedral_angle_d14.692950
X-RAY DIFFRACTIONf_chiral_restr0.031474
X-RAY DIFFRACTIONf_plane_restr0.003487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4249-3.60530.31341120.25351001X-RAY DIFFRACTION70
3.6053-3.83110.32881420.24661283X-RAY DIFFRACTION90
3.8311-4.12670.31671430.26151296X-RAY DIFFRACTION90
4.1267-4.54160.29731430.26281287X-RAY DIFFRACTION90
4.5416-5.19780.24341400.26591301X-RAY DIFFRACTION90
5.1978-6.54510.25341420.26611290X-RAY DIFFRACTION90
6.5451-43.40560.26991450.25851290X-RAY DIFFRACTION90

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