3AEM | pdb_00003aem

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing Michaelis complex and methionine imine-pyridoxamine-5'-phosphate

PDB DOI: https://doi.org/10.2210/pdb3AEM/pdb

Classification: LYASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-10 Released: 2011-02-09
Deposition Author(s): Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.196 (Depositor), 0.208 (DCC)
R-Value Work:
0.151 (Depositor), 0.172 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Entamoeba histolytica methionine gamma-lyase 1

Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.

To be published.

Macromolecule Content

Total Structure Weight: 171.48 kDa
Atom Count: 12,782
Modeled Residue Count: 1,544
Deposited Residue Count: 1,556
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, D	389	Entamoeba histolytica	Mutation(s): 0 Gene Names: metg EC: 4.4.1.11 (PDB Primary Data), 2.5.1.160 (UniProt)
UniProt
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28 Go to UniProtKB: Q86D28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86D28
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	C	389	Entamoeba histolytica	Mutation(s): 0 Gene Names: metg EC: 4.4.1.11 (PDB Primary Data), 2.5.1.160 (UniProt)
UniProt
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28 Go to UniProtKB: Q86D28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86D28
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2LM Query on 2LM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D]	E [auth A], H [auth B], M [auth D]	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid C₁₃ H₁₉ N₂ O₇ P S RNHGWTJOZCEIDD-RVDMUPIBSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth D]
MET Query on MET Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], K [auth C], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C]	G [auth A], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	C	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.196 (Depositor), 0.208 (DCC)
R-Value Work: 0.151 (Depositor), 0.172 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.086	α = 90
b = 85.332	β = 101.9
c = 114.331	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection