6KIM | pdb_00006kim

Crystal structure of diamondback moth ryanodine receptor SPRY2 domain

PDB DOI: https://doi.org/10.2210/pdb6KIM/pdb

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

Deposited: 2019-07-19 Released: 2020-07-22
Deposition Author(s): Zhou, Y., Lin, L., Yuchi, Z.
Funding Organization(s): Ministry of Science and Technology (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of diamondback moth ryanodine receptor SPRY2 domain

Zhou, Y., Lin, L., Yuchi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 20.53 kDa
Atom Count: 1,421
Modeled Residue Count: 172
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor	A	180	Plutella xylostella	Mutation(s): 1
UniProt
Find proteins for I3VR32 (Plutella xylostella) Explore I3VR32 Go to UniProtKB: I3VR32
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3VR32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.025	α = 90
b = 37.637	β = 93.24
c = 67.476	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-07-22
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.