1yx2

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

Method: X-RAY DIFFRACTION

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

Aminomethyltransferase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCST_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–365； UniProt 1–362 Author chain B； PDBConstruct 4–365； UniProt 1–362

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	1yx2
Deposition date deposition_date	2005-02-19
Structure title title	Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis
Keywords keywords	;aminomethyltransferase, glycine cleavage system T protein, alpha-beta, beta-barrel, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSFERASE ;; TRANSFERASE
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.

1yx2__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yx2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yx2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.83 Å
Rg (electron density)	20.74 Å
Total Rg	21.68 Å
Atom count	2805
Residues	355
Excluded volume	50191 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yx2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yx2__assembly_2__model_1`	monomeric （1）	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	Aminomethyltransferase
Molecular weight formula_weight	40445.8 kDa
EC 编号 ec_number	2.1.2.10
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6482

SNAMLKRTPLFDLYKEYGGKTIDFGGWELPVQFSSIKKEHEAVRTAAGLFDVSHMGEVEVSGNDSLSFLQRLMTNDVSALTPGRAQYTAMCYPDGGTVDDLLIYQKGENRYLLVINASNIDKDLAWMKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAMHIWKKIIDAGDAYGLIPCGLGARDTLRFEANIPLYGQELTRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLVGLEMIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPFYKR

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yx2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d1yx2a2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.1 — Aminomethyltransferase beta-barrel domain

Domain ID domain_id	d1yx2b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d1yx2b2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.1 — Aminomethyltransferase beta-barrel domain

CATH v4.4 (8 domains)

Domain ID domain_id	1yx2A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	1yx2A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	1yx2A03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	1yx2A04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	1yx2B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	1yx2B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	1yx2B03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	1yx2B04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

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Unit-cell length a length_a	47.628 Å
Unit-cell length b length_b	88.095 Å
Unit-cell length c length_c	88.764 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	41.200 Å
R factor r_factor	0.2192
R_work r_work	0.2117
R_free r_free	0.2880

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

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

Aminomethyltransferase

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

1yx2__assembly_2__model_1

1yx2__assembly_2__model_1 | I(q)

1yx2__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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)

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

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

Aminomethyltransferase

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

1yx2__assembly_2__model_1

1yx2__assembly_2__model_1 | I(q)

1yx2__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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)