SAXSdb — 1dxm

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

H PROTEIN

PISUM SATIVUM

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCSH_PEA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 35–165 Author chain B； PDBConstruct 1–131； UniProt 35–165

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	1dxm
Deposition date deposition_date	2000-01-10
Structure title title	Reduced form of the H protein from glycine decarboxylase complex
Keywords keywords	OXIDOREDUCTASES(ACTING ON CH-NH2 DONOR), GLYCINE DECARBOXYLASE, MITOCHONDRIA; OXIDOREDUCTASES(ACTING ON CH-NH2 DONOR)
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.

1dxm__assembly_2__model_1

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

Download this curve (.dat)

1dxm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dxm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.30 Å
Rg (electron density)	13.98 Å
Total Rg	15.26 Å
Atom count	994
Residues	131
Excluded volume	17643 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dxm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dxm__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	H PROTEIN
Molecular weight formula_weight	13962.5 kDa
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	2133

SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVESVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELESLLGAKEYTKFCEEEDAAH

Source Source

Source organism organism	PISUM SATIVUM
Common name common_name	GARDEN PEA
NCBI taxonomy ID ncbi_taxonomy_id	3888
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	DIHYDROLIPOIC ACID
Molecular weight formula_weight	208.3 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	145

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dxma_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

Domain ID domain_id	d1dxmb_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (2 domains)

Domain ID domain_id	1dxmA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1dxmB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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Unit-cell length a length_a	56.410 Å
Unit-cell length b length_b	56.410 Å
Unit-cell length c length_c	135.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2600

Reduced form of the H protein from glycine decarboxylase complex

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

H PROTEIN

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

1dxm__assembly_2__model_1

1dxm__assembly_2__model_1 | I(q)

1dxm__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)

Reduced form of the H protein from glycine decarboxylase complex

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

H PROTEIN

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

1dxm__assembly_2__model_1

1dxm__assembly_2__model_1 | I(q)

1dxm__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)