SAXSdb — 2o2k

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

Methionine synthase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	METH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–342； UniProt 925–1265 Author chain B； PDBConstruct 2–342； UniProt 925–1265

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	2o2k
Deposition date deposition_date	2006-11-30
Structure title title	Crystal Structure of the Activation Domain of Human Methionine Synthase Isoform/Mutant D963E/K1071N
Keywords keywords	C-shaped, twisted anti-parallel beta sheet, beta-meander region, 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.

2o2k__assembly_1__model_1

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

Download this curve (.dat)

2o2k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o2k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.26 Å
Rg (electron density)	28.36 Å
Total Rg	29.11 Å
Atom count	5279
Residues	665
Excluded volume	93636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o2k__assembly_1__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2o2ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.173 — Methionine synthase activation domain-like
Superfamily Superfamily superfamily	d.173.1 — Methionine synthase activation domain-like
Family Family family	d.173.1.0 — automated matches

Domain ID domain_id	d2o2kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.173 — Methionine synthase activation domain-like
Superfamily Superfamily superfamily	d.173.1 — Methionine synthase activation domain-like
Family Family family	d.173.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2o2kA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	196 — Cobalamin-dependent Methionine Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Vitamin B12-dependent methionine synthase, activation domain

Domain ID domain_id	2o2kA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	288 — Cobalamin-dependent Methionine Synthase; domain 2
Homologous superfamily homologous superfamily	10 — Cobalamin-dependent Methionine Synthase, domain 2

Domain ID domain_id	2o2kB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	196 — Cobalamin-dependent Methionine Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Vitamin B12-dependent methionine synthase, activation domain

Domain ID domain_id	2o2kB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	288 — Cobalamin-dependent Methionine Synthase; domain 2
Homologous superfamily homologous superfamily	10 — Cobalamin-dependent Methionine Synthase, domain 2

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Unit-cell length a length_a	77.854 Å
Unit-cell length b length_b	90.051 Å
Unit-cell length c length_c	123.006 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2113
R_work r_work	0.2094
R_free r_free	0.2478

Description description	Methionine synthase
Molecular weight formula_weight	40527.7 kDa
EC 编号 ec_number	2.1.1.13
Mutation mutation	D963E/K1071N
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6655

Crystal Structure of the Activation Domain of Human Methionine Synthase Isoform/Mutant D963E/K1071N

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

Methionine synthase

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

2o2k__assembly_1__model_1

2o2k__assembly_1__model_1 | I(q)

2o2k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

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)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1195

Crystal Structure of the Activation Domain of Human Methionine Synthase Isoform/Mutant D963E/K1071N

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

Methionine synthase

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

2o2k__assembly_1__model_1

2o2k__assembly_1__model_1 | I(q)

2o2k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)