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- PDB-5wue: Structural basis for conductance through TRIC cation channels -

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Basic information

Entry
Database: PDB / ID: 5wue
TitleStructural basis for conductance through TRIC cation channels
ComponentsUncharacterized protein
KeywordsMEMBRANE PROTEIN / TRIC / cation channel / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homologyGlycine transporter / Glycine transporter / metal ion binding / plasma membrane / Glycine transporter domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSu, M. / Gao, F. / Mao, Y. / Li, D.L. / Guo, Y.Z. / Wang, X.H. / Bruni, R. / Kloss, B. / Hendrickson, W.A. / Chen, Y.H. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for conductance through TRIC cation channels.
Authors: Su, M. / Gao, F. / Yuan, Q. / Mao, Y. / Li, D.L. / Guo, Y. / Yang, C. / Wang, X.H. / Bruni, R. / Kloss, B. / Zhao, H. / Zeng, Y. / Zhang, F.B. / Marks, A.R. / Hendrickson, W.A. / Chen, Y.H.
History
DepositionDec 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,7171
Non-polymers961
Water1448
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4396
Polymers77,1513
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7820 Å2
ΔGint-127 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.872, 115.872, 134.753
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Uncharacterized protein / prokaryotic SaTRIC


Mass: 25716.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00310, ATZ20_03355 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: A0A0U3H1E6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 69.7 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 7 / Details: PEG 200 40%, Li2SO4, 100mM, HEPES pH 7.0 100mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.91532 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91532 Å / Relative weight: 1
ReflectionResolution: 2.4→47.06 Å / Num. obs: 23120 / % possible obs: 89.2 % / Redundancy: 25.9 % / Biso Wilson estimate: 55.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0201 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.620.30.24320.47194.6
9.02-47.0623.40.0670.998199.3

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHENIXdev_2481refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WUC

5wuc


Resolution: 2.4→36.509 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2527 1125 4.87 %
Rwork0.2248 --
obs0.2261 23120 87.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.93 Å2 / Biso mean: 59.0801 Å2 / Biso min: 34.9 Å2
Refinement stepCycle: final / Resolution: 2.4→36.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 5 8 1530
Biso mean--79.72 60.85 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081552
X-RAY DIFFRACTIONf_angle_d0.9742119
X-RAY DIFFRACTIONf_chiral_restr0.055267
X-RAY DIFFRACTIONf_plane_restr0.006256
X-RAY DIFFRACTIONf_dihedral_angle_d13.888530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4003-2.50950.37771280.32582581270982
2.5095-2.64180.33311330.31272922305594
2.6418-2.80730.2822960.249919062002100
2.8073-3.02390.30711620.239331343296100
3.0239-3.3280.28151680.240731313299100
3.328-3.80920.27491210.22022315243674
3.8092-4.79740.24471530.20882860301391
4.7974-36.51360.19931640.203431463310100

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