8FZ9 | pdb_00008fz9

Crystal Structure of Bacillus cereus TIR protein

PDB DOI: https://doi.org/10.2210/pdb8FZ9/pdb

Classification: CHAPERONE
Organism(s): Bacillus cereus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-27 Released: 2024-06-19
Deposition Author(s): Khudaverdyan, N., Song, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.194 (Depositor), 0.190 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Toll/interleukin-1 receptor like protein from Bacillus cereus (BcTir)

Khudaverdyan, N., Song, J.

To be published.

Macromolecule Content

Total Structure Weight: 31.97 kDa
Atom Count: 2,504
Modeled Residue Count: 266
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR	A, B	138	Bacillus cereus	Mutation(s): 0
UniProt
Find proteins for A0AAT8XU12 (Bacillus cereus) Explore A0AAT8XU12 Go to UniProtKB: A0AAT8XU12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAT8XU12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.194 (Depositor), 0.190 (DCC)
R-Value Work: 0.161 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.695	α = 102.27
b = 38.285	β = 95.75
c = 66.822	γ = 101.91

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Khudaverdyan, N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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.