4DZR | pdb_00004dzr

The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

• PDB DOI: https://doi.org/10.2210/pdb4DZR/pdb

• Classification: TRANSFERASE
• Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-01 Released: 2012-03-14 
• Deposition Author(s): Tan, K., Chhor, G., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.269 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

Tan, K., Chhor, G., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.99 kDa 
• Atom Count: 1,271 
• Modeled Residue Count: 163 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-(Glutamine-N5) methyltransferase, release factor-specific	A	215	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0  Gene Names: Aaci_2779 EC: 2.1.1.297
UniProt
Find proteins for C8WUG7 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WUG7  Go to UniProtKB:  C8WUG7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.269 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.766	α = 90
b = 61.766	β = 90
c = 122.379	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Tan, K., Chhor, G., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary