1E5F

METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS

PDB DOI: https://doi.org/10.2210/pdb1E5F/pdb

Classification: LYASE
Organism(s): Trichomonas vaginalis G3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-07-25 Released: 2001-07-19
Deposition Author(s): Goodall, G., Mottram, J.C., Coombs, G.H., Lapthorn, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.212
R-Value Work: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase

Goodall, G., Mottram, J.C., Coombs, G.H., Lapthorn, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 89.46 kDa
Atom Count: 6,649
Modelled Residue Count: 786
Deposited Residue Count: 808
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE GAMMA-LYASE	A, B	404	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: MGL1 EC: 4.4.1.11
UniProt
Find proteins for O15564 (Trichomonas vaginalis) Explore O15564 Go to UniProtKB: O15564
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15564
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.212
R-Value Work: 0.162
Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.258	α = 90
b = 88.258	β = 90
c = 217.849	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2001-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-07-19
Type: Initial release
Version 1.1: 2011-08-31
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2012-11-14
Changes: Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

1E5F

METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS

The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)