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- PDB-6j6o: Crystal structure of diamondback moth ryanodine receptor phosphor... -

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Basic information

Entry
Database: PDB / ID: 6j6o
TitleCrystal structure of diamondback moth ryanodine receptor phosphorylation domain(2836-3050)
ComponentsRyanodine receptor
KeywordsMETAL TRANSPORT / diamondback moth / ryanodine receptor / phosphorylation domain / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / intracellular calcium ion homeostasis
Similarity search - Function
Globin-like - #160 / 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/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain ...Globin-like - #160 / 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/IP3 receptor binding core, RIH domain superfamily / 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. / Globin-like / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsXu, T. / Lin, L. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China) China
CitationJournal: Bmc Biol. / Year: 2019
Title: Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites.
Authors: Xu, T. / Yuchi, Z.
History
DepositionJan 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5988
Polymers25,2051
Non-polymers3937
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.994, 55.994, 132.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ryanodine receptor /


Mass: 25205.070 Da / Num. of mol.: 1 / Fragment: phosphorylation domian / Mutation: D3023A, K3024A, K3027A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Gene: RyR / Production host: Escherichia coli (E. coli) / References: UniProt: I3NWV8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8M Ammonium citrate tribasic pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 21391 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.023 / Rrim(I) all: 0.072 / Χ2: 0.506 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.889.90.71510490.8140.2380.7540.58100
1.88-1.92100.58310510.890.1940.6150.58100
1.92-1.959.80.49210560.9120.1650.520.555100
1.95-1.999.70.39510330.9470.1340.4170.514100
1.99-2.049.20.30710410.960.1070.3250.504100
2.04-2.089.30.26210700.9760.090.2770.527100
2.08-2.149.90.21310420.9820.0710.2250.505100
2.14-2.19100.19110380.9870.0630.2020.491100
2.19-2.26100.16710730.9910.0560.1760.547100
2.26-2.339.70.1410490.9910.0470.1470.51100
2.33-2.419.60.1210580.9930.0410.1270.523100
2.41-2.519.10.10510550.9940.0360.1110.503100
2.51-2.639.70.09110730.9960.0310.0960.503100
2.63-2.76100.07910700.9970.0260.0830.516100
2.76-2.949.90.06710730.9980.0230.0710.498100
2.94-3.169.40.05810680.9980.020.0620.511100
3.16-3.489.40.04610930.9990.0160.0490.502100
3.48-3.999.90.04110870.9990.0130.0430.501100
3.99-5.0290.03511080.9990.0120.0370.4399.9
5.02-508.80.03112040.9990.0110.0330.32299.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ETV, 5C30

4etv

5c30


Resolution: 1.848→32.666 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2337 2003 9.38 %
Rwork0.1858 --
obs0.1904 21343 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.16 Å2 / Biso mean: 30.2591 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: final / Resolution: 1.848→32.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 38 179 1775
Biso mean--47.73 37.46 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8482-1.89450.36591370.30251339147699
1.8945-1.94570.26221400.234213581498100
1.9457-2.00290.25131420.201813601502100
2.0029-2.06760.28751440.195313541498100
2.0676-2.14140.24981410.196213581499100
2.1414-2.22720.26961390.189413571496100
2.2272-2.32850.23471440.193413671511100
2.3285-2.45120.24781410.193613751516100
2.4512-2.60470.27311390.199113721511100
2.6047-2.80580.24191460.191313871533100
2.8058-3.08790.24511420.188313821524100
3.0879-3.53430.25141450.167314061551100
3.5343-4.4510.18691500.153214151565100
4.451-32.67120.19731530.191415101663100

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