3G05 | pdb_00003g05

Crystal structure of N-terminal domain (2-550) of E.coli MnmG

• PDB DOI: https://doi.org/10.2210/pdb3G05/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli O157:H7 str. EDL933
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-27 Released: 2009-10-20 
• Deposition Author(s): Shi, R., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme.

Shi, R., Villarroya, M., Ruiz-Partida, R., Li, Y., Proteau, A., Prado, S., Moukadiri, I., Benitez-Paez, A., Lomas, R., Wagner, J., Matte, A., Velazquez-Campoy, A., Armengod, M.E., Cygler, M.

(2009) J Bacteriol 191: 7614-7619

• PubMed: 19801413 
• DOI: https://doi.org/10.1128/JB.00650-09
• Primary Citation Related Structures: 
  3CES, 3G05


• PubMed Abstract: 
  

  The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-A resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montreal, Quebec, Canada.

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: 128.28 kDa 
• Atom Count: 8,156 
• Modeled Residue Count: 1,051 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG	A, B	576	Escherichia coli O157:H7 str. EDL933	Mutation(s): 0  Gene Names: ECs4683, gidA, mnmG, Z5241
UniProt
Find proteins for Q8XAY0 (Escherichia coli O157:H7) Explore Q8XAY0  Go to UniProtKB:  Q8XAY0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.593	α = 90
b = 144.593	β = 90
c = 271.019	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Shi, R., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description