7LJP

Structure of Thermotoga maritima SmpB

• PDB DOI: https://doi.org/10.2210/pdb7LJP/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-29 Released: 2022-02-09 
• Deposition Author(s): Chan, C.W., Mondragon, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Crystal structure of Thermotoga maritima SmpB reveals its C-terminal tail domain in a helical conformation mimicking that of a ribosome-bound state

Chan, C.W., Mondragon, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.35 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 419 
• Deposited Residue Count: 483 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SsrA-binding protein	A, B, C	161	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: smpB, TM_0254
UniProt
Find proteins for P56944 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore P56944  Go to UniProtKB:  P56944

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], W [auth C], X [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L [auth A], Q [auth B], R [auth B], S [auth B], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], T [auth C], U [auth C], V [auth C]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.539	α = 90
b = 92.539	β = 90
c = 307.943	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
Coot	model building
BUCCANEER	model building
PHASER	phasing
Aimless	data scaling
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Chan, C.W., Mondragon, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM058443
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118108
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008152
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008382

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description