2I6D | pdb_00002i6d

The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.

• PDB DOI: https://doi.org/10.2210/pdb2I6D/pdb

• Classification: TRANSFERASE
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-28 Released: 2006-10-17 
• Deposition Author(s): Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.235 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.

Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 28.45 kDa 
• Atom Count: 2,332 
• Modeled Residue Count: 251 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA methyltransferase, TrmH family	A	257	Porphyromonas gingivalis W83	Mutation(s): 6  Gene Names: SpoU, PG_0744 EC: 2.1.1
UniProt
Find proteins for Q7MW92 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MW92  Go to UniProtKB:  Q7MW92

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-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: 1.85 Å
• R-Value Free:  0.235 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.921	α = 90
b = 107.119	β = 90
c = 120.352	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary