3DXY | pdb_00003dxy

Crystal structure of EcTrmB in complex with SAM

• PDB DOI: https://doi.org/10.2210/pdb3DXY/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-25 Released: 2009-05-19 
• Deposition Author(s): Zhou, H.H., Liu, Q., Gao, Y.X., Teng, M.K., Niu, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion

Zhou, H., Liu, Q., Yang, W., Gao, Y., Teng, M., Niu, L.

(2009) Proteins 76: 512-515

• PubMed: 19373903 
• DOI: https://doi.org/10.1002/prot.22413
• Primary Citation Related Structures: 
  3DXX, 3DXY, 3DXZ

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Organizational Affiliation: 
• University of Science & Technology of China, Hefei, Anhui, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.6 kDa 
• Atom Count: 2,069 
• Modeled Residue Count: 207 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase	A	218	Escherichia coli K-12	Mutation(s): 0  Gene Names: trmB EC: 2.1.1.33
UniProt
Find proteins for P0A8I5 (Escherichia coli (strain K12)) Explore P0A8I5  Go to UniProtKB:  P0A8I5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.04	α = 90
b = 46.76	β = 90.4
c = 58.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Zhou, H.H., Liu, Q., Gao, Y.X., Teng, M.K., Niu, L.W.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description