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- PDB-6kim: Crystal structure of diamondback moth ryanodine receptor SPRY2 domain -

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Basic information

Entry
Database: PDB / ID: 6kim
TitleCrystal structure of diamondback moth ryanodine receptor SPRY2 domain
ComponentsRyanodine receptor
KeywordsTRANSPORT PROTEIN / diamondback moth / ryanodine receptor / ion channel / transport protein.
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / membrane => GO:0016020
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor ...Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.057 Å
AuthorsZhou, Y. / Lin, L. / Yuchi, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFD0201400 China
Ministry of Science and Technology (China)2017YFD0201403 China
CitationJournal: To Be Published
Title: Crystal structure of diamondback moth ryanodine receptor SPRY2 domain
Authors: Zhou, Y. / Lin, L. / Yuchi, Z.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5265
Polymers20,1571
Non-polymers3684
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monemer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.025, 37.637, 67.476
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ryanodine receptor /


Mass: 20157.326 Da / Num. of mol.: 1 / Mutation: K1242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Production host: Escherichia coli (E. coli) / References: UniProt: I3VR32
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Sodium/Potassium phosphate, Ph 6.5.

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.057→29.903 Å / Num. obs: 10749 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.3
Reflection shellResolution: 2.057→2.1656 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 162

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P9J

4p9j


Resolution: 2.057→29.903 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.62
RfactorNum. reflection% reflection
Rfree0.2513 1041 10.22 %
Rwork0.1864 --
obs0.1928 10187 94.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.52 Å2 / Biso mean: 27.2874 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 2.057→29.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 56 89 1444
Biso mean--50.69 33.04 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0572-2.16560.30831260.2012114884
2.1656-2.30130.26731430.1906125492
2.3013-2.47890.30871400.1945128994
2.4789-2.72820.27711600.2043131095
2.7282-3.12260.28651560.198134298
3.1226-3.93270.22261590.1754137199
3.9327-29.9030.2181570.1771143299

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