3EGE

Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EGE/pdb

• Classification: TRANSFERASE
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-10 Released: 2008-10-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.95 kDa 
• Atom Count: 2,124 
• Modelled Residue Count: 247 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase from antibiotic biosynthesis pathway	A	261	Trichormus variabilis ATCC 29413	Mutation(s): 0  Gene Names: YP_324569.1, Ava_4070
UniProt
Find proteins for Q3M5R2 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3M5R2  Go to UniProtKB:  Q3M5R2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M33EGE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.609	α = 90
b = 76.609	β = 90
c = 134.815	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations