6PI9 | pdb_00006pi9

Crystal structure of 16S rRNA methyltransferase RmtF in complex with S-Adenosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb6PI9/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-26 Released: 2019-07-10 
• Deposition Author(s): Stogios, P.J., Kim, Y., Evdokimova, E., Di Leo, R., Semper, C., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 16S rRNA methylase RmtF in complex with S-Adenosyl-L-homocysteine

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.14 kDa 
• Atom Count: 2,282 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA (guanine(1405)-N(7))-methyltransferase	A	260	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: rmtF, pN11x00042NDM_104 EC: 2.1.1.179
UniProt
Find proteins for I1YZZ5 (Klebsiella pneumoniae) Explore I1YZZ5  Go to UniProtKB:  I1YZZ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.637	α = 90
b = 77.637	β = 90
c = 96.926	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Stogios, P.J., Kim, Y., Evdokimova, E., Di Leo, R., Semper, C., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Structure summary
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description