2IGT

Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.192 
  • 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 the SAM Dependent Methyltransferase from Agrobacterium tumefaciens

Kim, Y.Joachimiak, A.Xu, X.Gu, J.Edwards, A.Savchenko, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAM dependent methyltransferase
A, B, C
332Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Find proteins for A9CKD6 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  A9CKD6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, C
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B, C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.941α = 90.00
b = 145.555β = 90.00
c = 204.895γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
Cootmodel building
SHELXCDphasing
SBC-Collectdata collection
HKL-2000data collection
SHELXEmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
MLPHAREphasing
HKL-3000phasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description