SAXSdb — 1wop

▼

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

Aminomethyltransferase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCST_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–364； UniProt 1–364

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1wop
Deposition date deposition_date	2004-08-24
Structure title title	Crystal Structure of T-protein of the Glycine Cleavage System
Keywords keywords	Aminomethyltransferase, T-protein, folinic acid, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1wop__assembly_1__model_1

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

Download this curve (.dat)

1wop__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wop__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.49 Å
Rg (electron density)	20.47 Å
Total Rg	21.42 Å
Atom count	2889
Residues	362
Excluded volume	51856 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wop__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Aminomethyltransferase
Molecular weight formula_weight	40381.4 kDa
EC 编号 ec_number	2.1.2.10
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3152

MKRTPLFEKHVELGAKMVDFAGWEMPLYYTSIFEEVMAVRKSVGMFDVSHMGEFLVKGPEAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKDFNWIKSHSKNFDVEVSNISDTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLEATYLLYGQDMDENTNPFEVGLSWVVKLNKDFVGKEALLKAKEKVERKLVALELSGKRIARKGYEVLKNGERVGEITSGNFSPTLGKSIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSVRREV

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
Molecular weight formula_weight	473.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wopa1
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	d1wopa2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1wopA01
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	1wopA02
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	1wopA03
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	1wopA04
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

▶

Unit-cell length a length_a	52.846 Å
Unit-cell length b length_b	54.091 Å
Unit-cell length c length_c	149.240 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	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2570

Crystal Structure of T-protein of the Glycine Cleavage System

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

1wop__assembly_1__model_1

1wop__assembly_1__model_1 | I(q)

1wop__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of T-protein of the Glycine Cleavage System

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

1wop__assembly_1__model_1

1wop__assembly_1__model_1 | I(q)

1wop__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)