4IG6 | pdb_00004ig6

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine

• PDB DOI: https://doi.org/10.2210/pdb4IG6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Anaplasma phagocytophilum str. HZ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-16 Released: 2012-12-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.204 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine

Edwards, T.E., Clifton, M.C., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Macromolecule Content 

• Total Structure Weight: 28.53 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 223 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	253	Anaplasma phagocytophilum str. HZ	Mutation(s): 0  Gene Names: APH_1267, trmD EC: 2.1.1.228
UniProt
Find proteins for Q2GIL5 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GIL5  Go to UniProtKB:  Q2GIL5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.204 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.11	α = 90
b = 105.11	β = 90
c = 92.25	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description