6LT9 | pdb_00006lt9

The crystal structure of diamondback moth ryanodine receptor SPRY1 domain

PDB DOI: https://doi.org/10.2210/pdb6LT9/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Plutella xylostella
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-01-22 Released: 2021-01-27
Deposition Author(s): Zhou, Y., Lin, L., Yuchi, Z.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of diamondback moth ryanodine receptor SPRY1 domain

Nayak, B., Zhou, Y., Salauddin, N., Lin, L., You, M., You, S., Yuchi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 43.52 kDa
Atom Count: 2,992
Modeled Residue Count: 362
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A [auth F], B	195	Plutella xylostella	Mutation(s): 2
UniProt
Find proteins for G8EME3 (Plutella xylostella) Explore G8EME3 Go to UniProtKB: G8EME3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8EME3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth F] SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth F] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth F] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	C [auth F], E [auth B], F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth F] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth F] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth F] SDF format, chain H [auth B] MOL2 format, chain D [auth F] MOL2 format, chain H [auth B] mmCIF format, chain D [auth F] mmCIF format, chain H [auth B]	D [auth F], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth F] Focus chain H [auth B] Interactions & Density Focus chain D [auth F] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216 (Depositor), 0.215 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.893	α = 90
b = 64.893	β = 90
c = 95.767	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFD0201400
Ministry of Science and Technology (MoST, China)	China	2017YFD0201403

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.