3G5T | pdb_00003g5t

Crystal structure of trans-aconitate 3-methyltransferase from yeast

• PDB DOI: https://doi.org/10.2210/pdb3G5T/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-05 Released: 2009-03-03 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.137 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Literature

Crystal structure of trans-aconitate 3-methyltransferase from yeast

Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N.

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: 36.2 kDa 
• Atom Count: 3,243 
• Modeled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trans-aconitate 3-methyltransferase	A	299	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: P32643, S000000977, SYGP-ORF63, TAM1, TMT1, YER175C EC: 2.1.1.145
UniProt
Find proteins for P32643 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32643  Go to UniProtKB:  P32643

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	J [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
T8N	K [auth A]	(2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid C7 H8 O6 MRNZYUAGJLJQAM-DUXPYHPUSA-N
DMS	L [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [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: 1.12 Å
• R-Value Free:  0.137 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.834	α = 90
b = 91.891	β = 90
c = 104.269	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary