4N05 | pdb_00004n05

The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482

• PDB DOI: https://doi.org/10.2210/pdb4N05/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-10-01 Released: 2013-12-04 
• Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482

Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 74.14 kDa 
• Atom Count: 4,751 
• Modeled Residue Count: 560 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ryanodine receptor	A [auth B], B [auth A], C, D, E, F	103	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1  Gene Names: BT_2247
UniProt
Find proteins for Q8A5J2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5J2  Go to UniProtKB:  Q8A5J2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B], H [auth A], I [auth A], J [auth C], K [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B], B [auth A], C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.362	α = 90
b = 88.673	β = 111
c = 74.37	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary