3G5T

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.137
R-Value Work: 0.120
R-Value Observed: 0.121

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 36.2 kDa
Atom Count: 3,243
Modelled Residue Count: 299
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32643
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
T8N Query on T8N Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	(2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid C₇ H₈ O₆ MRNZYUAGJLJQAM-DUXPYHPUSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.120
R-Value Observed: 0.121
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