SAXSdb — 7e37

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

Deoxypodophyllotoxin synthase

Sinopodophyllum hexandrum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 2-OXOGLUTARIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 2-OXOGLUTARIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	2ODD_SINHE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 1–310 Author chain B； PDBConstruct 1–310； UniProt 1–310

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	7e37
Deposition date deposition_date	2021-02-08
Structure title title	Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate
Keywords keywords	;non-heme iron/2-oxoglutarate enzyme beta-helix fold deoxypodophyllotoxin biosynthesis carbon-carbon bond formation, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC PROTEIN
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.

7e37__assembly_2__model_1

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

Download this curve (.dat)

7e37__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7e37__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.50 Å
Rg (electron density)	19.22 Å
Total Rg	20.10 Å
Atom count	2462
Residues	305
Excluded volume	43715 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7e37__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7e37__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 (4)

Entity 1 Entity 1 polymer

Description description	Deoxypodophyllotoxin synthase
Molecular weight formula_weight	36140.1 kDa
EC 编号 ec_number	1.14.20.8
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	5398

MGSTAPLRLPVIDLSMKNLKPGTTSWNSVRTQVREALEEYGCFEAVIDAVSPELQKAVCNKGHELLNLPLETKMLNGNKPEYDGFTSIPNLNEGMGVGRITDLEKVERFTNLMWPEGNKDFCETVYSYGKRMAEVDHILKMMVFESFGMEKHFDSFCESTNYLLHFMRYQQPGKDGRSPALSLHKDKSILTIVNQNDVKGLEFETKDGEWILPTADNHIVLLGDCFMAWSNGRLHSPLHRVTLVANQARLSTSSFSFPKDIIETPAELVDEEHPLLFNPFEITELLAYCFTKEGAKAVCDLKQYKAYTGALEHHHHHH

Source Source

Source organism organism	Sinopodophyllum hexandrum
Common name common_name	Himalayan may apple
NCBI taxonomy ID ncbi_taxonomy_id	93608
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 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	467

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7e37A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	330 — B-lactam Antibiotic, Isopenicillin N Synthase; Chain

Domain ID domain_id	7e37B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	330 — B-lactam Antibiotic, Isopenicillin N Synthase; Chain

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Unit-cell length a length_a	101.050 Å
Unit-cell length b length_b	158.287 Å
Unit-cell length c length_c	51.874 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	27.020 Å
R factor r_factor	0.1951
R_work r_work	0.1932
R_free r_free	0.2380

Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate

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

Deoxypodophyllotoxin 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

7e37__assembly_2__model_1

7e37__assembly_2__model_1 | I(q)

7e37__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 (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

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate

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

Deoxypodophyllotoxin 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

7e37__assembly_2__model_1

7e37__assembly_2__model_1 | I(q)

7e37__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 (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

CATH v4.4 (2 domains)

7. Citations (1)