3GGD

Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 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 methyltransferase
A
245Anabaena variabilis (strain ATCC 29413 / PCC 7937)Mutation(s): 0 
Find proteins for Q3M3X1 (Anabaena variabilis (strain ATCC 29413 / PCC 7937))
Go to UniProtKB:  Q3M3X1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 112.520α = 90.00
b = 112.520β = 90.00
c = 112.560γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
autoSHARPphasing
SHELXDphasing
SHELXphasing
MolProbitymodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description