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- PDB-5wtr: Crystal structure of a prokaryotic TRIC channel in 0.5 M KCl -

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Basic information

Entry
Database: PDB / ID: 5wtr
TitleCrystal structure of a prokaryotic TRIC channel in 0.5 M KCl
ComponentsUncharacterized protein
KeywordsMEMBRANE PROTEIN / Mambrane protein / ion channel
Function / homologyGlycine transporter / Glycine transporter / plasma membrane / : / TRISTEAROYLGLYCEROL / Glycine transporter domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsOu, X.M. / Wang, L.F. / Yang, H.T. / Liu, X.Y. / Liu, Z.F.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020302 China
Ministry of Science and Technology2014CB910301 China
Office of Global Experts RecruitmentNational Thousand Young Talents Program China
CitationJournal: BMC BIOL. / Year: 2017
Title: Ion and water binding sites inside an occluded hourglass pore of a TRIC channel
Authors: Ou, X.M. / Guo, J.L. / Wang, L.F. / Yang, H.T. / Liu, X.Y. / Sun, J.Y. / Liu, Z.F.
History
DepositionDec 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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.ptnr1_symmetry / _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.ptnr2_symmetry / _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 / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,24553
Polymers140,4276
Non-polymers3,81847
Water6,864381
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,10326
Polymers70,2143
Non-polymers1,88923
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-74 kcal/mol
Surface area21630 Å2
MethodPISA
2
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,14227
Polymers70,2143
Non-polymers1,92924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-72 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.073, 87.730, 173.062
Angle α, β, γ (deg.)90.00, 108.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-308-

K

21B-425-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 23404.502 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0012 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q981D4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C57H110O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 3.89 Å3/Da / Density % sol: 68.37 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Well solution: 22-26% PEG 3000, 0.1 M Tris-HCl pH8.0, 0.2 M NaAc, 0.2 M KCl Before being frozen, the crystals were washed and soaked in 26% PEG3000, 50 mM Tris-HCl pH 8.0, 1.1% OG, 0.1% DM, ...Details: Well solution: 22-26% PEG 3000, 0.1 M Tris-HCl pH8.0, 0.2 M NaAc, 0.2 M KCl Before being frozen, the crystals were washed and soaked in 26% PEG3000, 50 mM Tris-HCl pH 8.0, 1.1% OG, 0.1% DM, 3% ethylene glycol, 0.5 M KCl
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00137 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00137 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 106700 / % possible obs: 97.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.149 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.7 / % possible all: 94.8

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Processing

Software
NameVersionClassification
CNS1.3refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cross valid method: FREE R-VALUE
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 2614 2.4 %Random selection
Rwork0.2108 ---
obs-106561 97.4 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 38.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9054 0 207 381 9642
LS refinement shellResolution: 2.2→2.21 Å /
RfactorNum. reflection
Rfree0.2862 45
Rwork0.2814 1966

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