3D2L

Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAM-dependent methyltransferaseA, B, C, D243Exiguobacterium sibiricum 255-15Mutation(s): 0 
Gene Names: ZP_00538691.1ExigDRAFT_1659Exig_0770
Find proteins for B1YKR8 (Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15))
Explore B1YKR8 
Go to UniProtKB:  B1YKR8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M33D2L Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.83α = 116.57
b = 70.92β = 104.63
c = 77.19γ = 102.32
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description