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- PDB-6iyu: Crystal Structure Analysis of an Eukaryotic Membrane Protein -

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Basic information

Entry
Database: PDB / ID: 6iyu
TitleCrystal Structure Analysis of an Eukaryotic Membrane Protein
ComponentsTrimeric intracellular cation channel type A
KeywordsMEMBRANE PROTEIN / TRIC / cation channel
Function / homologyTRIC channel / TRIC channel / potassium channel activity / sarcoplasmic reticulum membrane / nuclear membrane / identical protein binding / Trimeric intracellular cation channel type A
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.199 Å
AuthorsWang, X.H. / Zeng, Y. / Su, M. / Gao, F. / 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 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7387
Polymers37,5201
Non-polymers2176
Water1,35175
1
A: Trimeric intracellular cation channel type A
hetero molecules

A: Trimeric intracellular cation channel type A
hetero molecules

A: Trimeric intracellular cation channel type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,21321
Polymers112,5613
Non-polymers65218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7650 Å2
ΔGint-221 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.449, 127.449, 102.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21A-518-

HOH

31A-540-

HOH

41A-553-

HOH

51A-574-

HOH

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Components

#1: Protein Trimeric intracellular cation channel type A / TRICA / Transmembrane protein 38A


Mass: 37520.281 Da / Num. of mol.: 1 / Mutation: C245S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TMEM38A, RCJMB04_13f15 / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q5ZK43
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→48.55 Å / Num. obs: 25429 / % possible obs: 100 % / Redundancy: 37.5 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.018 / Rrim(I) all: 0.111 / Net I/σ(I): 28.6 / Num. measured all: 954527
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2737.52.4638099121590.6920.4052.4972.299.9
9.07-48.5528.50.0441263644410.0080.04510299.3

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.199→41.717 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1294 5.09 %
Rwork0.1983 24107 -
obs0.1993 25401 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.78 Å2 / Biso mean: 60.2731 Å2 / Biso min: 29.33 Å2
Refinement stepCycle: final / Resolution: 2.199→41.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 6 75 1885
Biso mean--62.69 62.96 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1992-2.28720.25111350.239226162751
2.2872-2.39130.23631420.215226182760
2.3913-2.51740.25311440.19926352779
2.5174-2.67510.21021540.170226282782
2.6751-2.88150.16581450.150326282773
2.8815-3.17140.16841470.161126662813
3.1714-3.63010.16871520.165526902842
3.6301-4.57270.20111490.18327092858
4.5727-41.7250.28221260.241429173043
Refinement TLS params.Method: refined / Origin x: 44.9851 Å / Origin y: 29.4236 Å / Origin z: 44.0854 Å
111213212223313233
T0.3235 Å2-0.0222 Å20.1021 Å2-0.394 Å2-0.0121 Å2--0.3849 Å2
L0.5395 °2-0.1024 °2-0.1037 °2-0.4395 °2-0.1329 °2--0.4665 °2
S-0.0809 Å °-0.1866 Å °-0.1838 Å °0.1852 Å °-0.0521 Å °0.3706 Å °0.0705 Å °-0.2544 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 231
2X-RAY DIFFRACTION1allS1 - 94
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1 - 5

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