SAXSdb — 1lt7

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

BETAINE-HOMOCYSTEINE METHYLTRANSFERASE

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SAMARIUM (III) ION × 8 CITRIC ACID × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SAMARIUM (III) ION × 4 CITRIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BHMT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–406； UniProt 1–406 Author chain B； PDBConstruct 1–406； UniProt 1–406

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	1lt7
Deposition date deposition_date	2002-05-20
Structure title title	Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions
Keywords keywords	TRANSFERASE, homocysteine metabolism, homocysteinemia, thiol alkyl transfer; 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.

1lt7__assembly_1__model_1

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

Download this curve (.dat)

1lt7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lt7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.33 Å
Rg (electron density)	34.97 Å
Total Rg	35.53 Å
Atom count	9696
Residues	1240
Excluded volume	172930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lt7__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1lt7__assembly_2__model_1`	dimeric （2）	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	BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
Molecular weight formula_weight	44844.0 kDa
EC 编号 ec_number	2.1.1.5
Mutation mutation	P2A, C104A, C131A, C186A, C201A, C256A
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	5146

MAPVGGKKAKKGILERLNAGEIVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFYASEDKLENRGNYVLEKISGQEVNEAAADIARQVADEGDALVAGGVSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMAIGPEGDLHGVPPGEAAVRLVKAGASIIGVNCHFDPTISLKTVKLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWENLRIASGRPYNPSMSKPDGWGVTKGTAELMQQKEATTEQQLKELFEKQKFKSQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SAMARIUM (III) ION
Molecular weight formula_weight	150.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lt7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
Family Family family	c.1.26.1 — Homocysteine S-methyltransferase

Domain ID domain_id	d1lt7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
Family Family family	c.1.26.1 — Homocysteine S-methyltransferase

CATH v4.4 (2 domains)

Domain ID domain_id	1lt7A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	330 — Homocysteine-binding-like domain

Domain ID domain_id	1lt7B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	330 — Homocysteine-binding-like domain

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Unit-cell length a length_a	109.990 Å
Unit-cell length b length_b	90.085 Å
Unit-cell length c length_c	89.085 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.10 °
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	2.150 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	0.2180
R_work r_work	0.2030
R_free r_free	0.2490

Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions

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

BETAINE-HOMOCYSTEINE METHYLTRANSFERASE

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

1lt7__assembly_1__model_1

1lt7__assembly_1__model_1 | I(q)

1lt7__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions

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

BETAINE-HOMOCYSTEINE METHYLTRANSFERASE

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

1lt7__assembly_1__model_1

1lt7__assembly_1__model_1 | I(q)

1lt7__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)