8DDP | pdb_00008ddp

Crystal structure of SRS57 from Toxoplasma gondii

PDB DOI: https://doi.org/10.2210/pdb8DDP/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Toxoplasma gondii ME49
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-06-18 Released: 2023-07-05
Deposition Author(s): Ramaswamy, R., Boulanger, M.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of SRS29C from Toxoplasma gondii

Ramaswamy, R., Boulanger, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 31.32 kDa
Atom Count: 2,524
Modeled Residue Count: 277
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAG-related sequence SRS57	A	279	Toxoplasma gondii ME49	Mutation(s): 0 Gene Names: SRS57, TGME49_308020
UniProt
Find proteins for A0A125YY85 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore A0A125YY85 Go to UniProtKB: A0A125YY85
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125YY85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.191 (Depositor), 0.200 (DCC)
R-Value Work: 0.169 (Depositor), 0.180 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.13	α = 90
b = 59.71	β = 90
c = 101.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Boulanger, M.J.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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.