2P35 | pdb_00002p35

Crystal structure of trans-aconitate methyltransferase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2P35/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-08 Released: 2007-04-10 
• Deposition Author(s): Chang, C., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of trans-aconitate methyltransferase from Agrobacterium tumefaciens

Chang, C., Xu, X., Zheng, H., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.01 kDa 
• Atom Count: 4,419 
• Modeled Residue Count: 485 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trans-aconitate 2-methyltransferase	A, B	259	Agrobacterium fabrum str. C58	Mutation(s): 7  Gene Names: tam, Atu0870, AGR_C_1589 EC: 2.1.1.144
UniProt
Find proteins for Q8UH15 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8UH15  Go to UniProtKB:  Q8UH15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.097	α = 90
b = 103.097	β = 90
c = 107.457	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Chang, C., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2007-11-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary