5BXY | pdb_00005bxy

Crystal structure of RNA methyltransferase from Salinibacter ruber in complex with S-Adenosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb5BXY/pdb

• Classification: TRANSFERASE
• Organism(s): Salinibacter ruber DSM 13855
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-09 Released: 2015-07-01 
• Deposition Author(s): Handing, K.B., LaRowe, C., Shabalin, I.G., Stead, M., Hillerich, B.S., Ahmed, M., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of RNA methylase family protein from Salinibacterruber in complex with S-Adenosyl-L-homocysteine.

Handing, K.B., LaRowe, C., Shabalin, I.G., Stead, M., Hillerich, B.S., Ahmed, M., Bonanno, J., Almo, S.C., Minor, W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.31 kDa 
• Atom Count: 2,763 
• Modeled Residue Count: 308 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA methyltransferase	A, B	158	Salinibacter ruber DSM 13855	Mutation(s): 0  Gene Names: SRU_1020 EC: 2.1.1
UniProt
Find proteins for Q2S3S9 (Salinibacter ruber (strain DSM 13855 / M31)) Explore Q2S3S9  Go to UniProtKB:  Q2S3S9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], G [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	D [auth A], E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35888

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.574	α = 90
b = 86.04	β = 90
c = 85.057	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data scaling
SCALEPACK	data scaling
HKL-3000	data reduction
MLPHARE	phasing
HKL-3000	phasing
DM	phasing
SHELX	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Handing, K.B., LaRowe, C., Shabalin, I.G., Stead, M., Hillerich, B.S., Ahmed, M., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary