1ukj

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine gamma-lyase

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEGL_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–398； UniProt 1–398 Author chain B； PDBConstruct 1–398； UniProt 1–398 Author chain C； PDBConstruct 1–398； UniProt 1–398 Author chain D； PDBConstruct 1–398； UniProt 1–398

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ukj
Deposition date deposition_date	2003-08-24
Structure title title	Detailed structure of L-Methionine-Lyase from Pseudomonas putida
Keywords keywords	Pyridoxal phosphate, Pseudomonas putida, methionine, lyase; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1ukj__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ukj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ukj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.88 Å
Rg (electron density)	33.17 Å
Total Rg	33.71 Å
Atom count	12069
Residues	1588
Excluded volume	213810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ukj__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Methionine gamma-lyase
Molecular weight formula_weight	42901.7 kDa
EC 编号 ec_number	4.4.1.11
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13148

MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1079

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ukja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1ukjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1ukjc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1ukjd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1ukjA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1ukjA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1ukjB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1ukjB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1ukjC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1ukjC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1ukjD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1ukjD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

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Unit-cell length a length_a	133.093 Å
Unit-cell length b length_b	133.093 Å
Unit-cell length c length_c	215.028 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1775
R_free r_free	0.2953

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine gamma-lyase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ukj__assembly_1__model_1

1ukj__assembly_1__model_1 | I(q)

1ukj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine gamma-lyase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ukj__assembly_1__model_1

1ukj__assembly_1__model_1 | I(q)

1ukj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)