3B89 | pdb_00003b89

Crystal structure of rRNA methylase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3B89/pdb

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


• Deposited: 2007-10-31 Released: 2007-11-27 
• Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.220 (DCC) 

Literature

Crystal structure of rRNA methylase from Escherichia coli.

Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

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: 28.01 kDa 
• Atom Count: 1,907 
• Modeled Residue Count: 240 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA methylase	A	252	Escherichia coli	Mutation(s): 0  Gene Names: rmtB EC: 2.1.1.179
UniProt
Find proteins for Q763K9 (Escherichia coli) Explore Q763K9  Go to UniProtKB:  Q763K9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	B [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-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: 2.60 Å
• R-Value Free:  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.220 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.262	α = 90
b = 94.131	β = 90
c = 96.23	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-27 
Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary