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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA methyltransferase
A, B
158Salinibacter ruber (strain DSM 13855 / M31)N/A
Find proteins for Q2S3S9 (Salinibacter ruber (strain DSM 13855 / M31))
Go to UniProtKB:  Q2S3S9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-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

Unit Cell:
Length (Å)Angle (°)
a = 43.574α = 90.00
b = 86.040β = 90.00
c = 85.057γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
Cootmodel building
SBC-Collectdata collection
REFMACrefinement
SHELXphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing
DMphasing
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy