5BXY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA methyltransferaseA, B158Salinibacter ruber DSM 13855Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2S3S9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.18430/M35888
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.574α = 90
b = 86.04β = 90
c = 85.057γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-2000data scaling
SCALEPACKdata scaling
HKL-3000data reduction
MLPHAREphasing
HKL-3000phasing
DMphasing
SHELXphasing
PDB_EXTRACTdata extraction
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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