SAXSdb — 2bgm

▼

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

RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE

PODOPHYLLUM PELTATUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) × 4 MATAIRESINOL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q94KL8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 1–278

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	2bgm
Deposition date deposition_date	2004-12-23
Structure title title	X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase
Keywords keywords	XIDOREDUCTASE, OXIDOREDUCTASE, DEHYDROGENASE; XIDOREDUCTASE
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.

2bgm__assembly_1__model_1

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

Download this curve (.dat)

2bgm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bgm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.41 Å
Rg (electron density)	28.19 Å
Total Rg	29.06 Å
Atom count	8220
Residues	1068
Excluded volume	146360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bgm__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
Molecular weight formula_weight	29285.2 kDa
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	2182

MGSTSTPDSSTNRLQDKVAIITGGAGGIGETTAKLFVRYGAKVVIADIADDHGQKVCNNIGSPDVISFVHCDVTKDEDVRNLVDTTIAKHGKLDIMFGNVGVLSTTPYSILEAGNEDFKRVMDINVYGAFLVAKHAARVMIPAKKGSIVFTASISSFTAGEGVSHVYTATKHAVLGLTTSLCTELGEYGIRVNCVSPYIVASPLLTDVFGVDSSRVEELAHQAANLKGTLLRAEDVADAVAYLAGDESKYVSGLNLVIDGGYTRTNPAFPTALKHGLA

Source Source

Source organism organism	PODOPHYLLUM PELTATUM
Common name common_name	MAYAPPLE
NCBI taxonomy ID ncbi_taxonomy_id	35933
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MATAIRESINOL
Molecular weight formula_weight	358.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2bgma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2bgmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

▶

Unit-cell length a length_a	57.350 Å
Unit-cell length b length_b	118.740 Å
Unit-cell length c length_c	131.250 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	16

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2290

X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase

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

RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE

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

2bgm__assembly_1__model_1

2bgm__assembly_1__model_1 | I(q)

2bgm__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase

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

RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE

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

2bgm__assembly_1__model_1

2bgm__assembly_1__model_1 | I(q)

2bgm__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)