SAXSdb — 9m2l

▼

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

Alpha-ketoglutarate-dependent dioxygenase

Penicillium simplicissimum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 2 ;(1Z,4R,12S,14S,17Z)-12-hydroxy-19,19-dimethyl-5-(2-methylbut-3-en-2-yl)-3,5,16,21-tetrazaheptacyclo[14.13.0.03,14.04,12.06,11.020,28.022,27]nonacosa-1(29),6,8,10,17,20(28),22,24,26-nonaene-2,15-dione ; × 2 2-OXOGLUTARIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 2 ;(1Z,4R,12S,14S,17Z)-12-hydroxy-19,19-dimethyl-5-(2-methylbut-3-en-2-yl)-3,5,16,21-tetrazaheptacyclo[14.13.0.03,14.04,12.06,11.020,28.022,27]nonacosa-1(29),6,8,10,17,20(28),22,24,26-nonaene-2,15-dione ; × 2 2-OXOGLUTARIC ACID × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 4 ;(1Z,4R,12S,14S,17Z)-12-hydroxy-19,19-dimethyl-5-(2-methylbut-3-en-2-yl)-3,5,16,21-tetrazaheptacyclo[14.13.0.03,14.04,12.06,11.020,28.022,27]nonacosa-1(29),6,8,10,17,20(28),22,24,26-nonaene-2,15-dione ; × 4 2-OXOGLUTARIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2Z5U507_PENSI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–305； UniProt 2–299 Author chain B； PDBConstruct 8–305； UniProt 2–299 Author chain C； PDBConstruct 8–305； UniProt 2–299 Author chain D； PDBConstruct 8–305； UniProt 2–299

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	9m2l
Deposition date deposition_date	2025-02-27
Structure title title	Crystal structure of okaE in complex with a-ketoglutarate and okaramine A at 2.5 angstroms resolution.
Keywords keywords	AKG-dependent mononuclear nonheme iron enzymes, multiple functions, okaramine indole alkaloids, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9m2l__assembly_1__model_1

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

Download this curve (.dat)

9m2l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9m2l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.14 Å
Rg (electron density)	25.14 Å
Total Rg	25.97 Å
Atom count	4659
Residues	579
Excluded volume	82079 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9m2l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9m2l__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9m2l__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Alpha-ketoglutarate-dependent dioxygenase
Molecular weight formula_weight	34222.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,B,C
Atom count atom_count	9675

GDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEMNQEFYQMPVPTTTKWMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGG

Source Source

Source organism organism	Penicillium simplicissimum
NCBI taxonomy ID ncbi_taxonomy_id	69488
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;(1Z,4R,12S,14S,17Z)-12-hydroxy-19,19-dimethyl-5-(2-methylbut-3-en-2-yl)-3,5,16,21-tetrazaheptacyclo[14.13.0.03,14.04,12.06,11.020,28.022,27]nonacosa-1(29),6,8,10,17,20(28),22,24,26-nonaene-2,15-dione ;
Molecular weight formula_weight	520.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	271

▶

Unit-cell length a length_a	76.121 Å
Unit-cell length b length_b	107.661 Å
Unit-cell length c length_c	134.569 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	43.950 Å
R factor r_factor	0.1872
R_work r_work	0.1848
R_free r_free	0.2319

Crystal structure of okaE in complex with a-ketoglutarate and okaramine A at 2.5 angstroms resolution.

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

Alpha-ketoglutarate-dependent dioxygenase

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

9m2l__assembly_1__model_1

9m2l__assembly_1__model_1 | I(q)

9m2l__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of okaE in complex with a-ketoglutarate and okaramine A at 2.5 angstroms resolution.

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

Alpha-ketoglutarate-dependent dioxygenase

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

9m2l__assembly_1__model_1

9m2l__assembly_1__model_1 | I(q)

9m2l__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)