SAXSdb — 1pff

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

methionine gamma-lyase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 42 DI(HYDROXYETHYL)ETHER × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O15565_TRIVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 68–398 Author chain B； PDBConstruct 1–330； UniProt 68–398

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	1pff
Deposition date deposition_date	2003-05-26
Structure title title	Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms
Keywords keywords	gamma-lyase, homocysteine, 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.

1pff__assembly_1__model_1

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

Download this curve (.dat)

1pff__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pff__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.29 Å
Rg (electron density)	34.53 Å
Total Rg	35.09 Å
Atom count	10286
Residues	1324
Excluded volume	185090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pff__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 (4)

Entity 1 Entity 1 polymer

Description description	methionine gamma-lyase
Molecular weight formula_weight	35934.5 kDa
EC 编号 ec_number	4.4.1.11
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5484

SALEGKIAKLEHAEACAATASGMGAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAVPGNIEKHLKPNTRIVYFETPANPTLKVIDIEDAVKQARKQKDILVIVDNTFASPILTNPLDLGVDIVVHSATKYINGHTDVVAGLVCSRADIIAKVKSQGIKDITGAIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEHKAVKKVYYPGLPDHPGHEIAKKQMKMFGSMIAFDVDGLEKAKKVLDNCHVVSLAVSLGGPESLIQHPASMTHAGVPKEEREAAGLTDNLIRLSVGCENVQDIIDDLKQALDLVL

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	339

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pffa_
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	d1pffb_
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 (4 domains)

Domain ID domain_id	1pffA01
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	1pffA02
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	1pffB01
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	1pffB02
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	166.634 Å
Unit-cell length b length_b	48.476 Å
Unit-cell length c length_c	75.606 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	32.500 Å
R factor r_factor	0.1797
R_work r_work	0.1791
R_free r_free	0.2084

Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms

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

1pff__assembly_1__model_1

1pff__assembly_1__model_1 | I(q)

1pff__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (0)

Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms

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

1pff__assembly_1__model_1

1pff__assembly_1__model_1 | I(q)

1pff__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (0)