SAXSdb — 9uag

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

Iron/alpha-ketoglutarate-dependent dioxygenase okaE

Penicillium simplicissimum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 4 2-OXOGLUTARIC ACID × 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 ; × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OKAE_PENOH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–307； UniProt 2–300 Author chain B； PDBConstruct 9–307； UniProt 2–300 Author chain C； PDBConstruct 9–307； UniProt 2–300 Author chain D； PDBConstruct 9–307； UniProt 2–300

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	9uag
Deposition date deposition_date	2025-03-31
Structure title title	Crystal structure of the OkaE-M71A mutant with a-ketoglutarate and okaramine A
Keywords keywords	dioxygenase, non-heme, iron dependent, oxidoreductase; OXIDOREDUCTASE
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.

9uag__assembly_1__model_1

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

Download this curve (.dat)

9uag__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9uag__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.00 Å
Rg (electron density)	34.25 Å
Total Rg	34.89 Å
Atom count	9249
Residues	1166
Excluded volume	163200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9uag__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Iron/alpha-ketoglutarate-dependent dioxygenase okaE
Molecular weight formula_weight	35439.2 kDa
EC 编号 ec_number	1.14.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9769

MGDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEMNQEFYQAPVPTTTKWMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGGCWSHPQFEK

Source Source

Source organism organism	Penicillium simplicissimum
NCBI taxonomy ID ncbi_taxonomy_id	69488
Host organism host_organism	Escherichia coli BL21(DE3)

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

Entity 4 Entity 4 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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	520

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Unit-cell length a length_a	76.414 Å
Unit-cell length b length_b	107.526 Å
Unit-cell length c length_c	134.525 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	38.670 Å
R factor r_factor	0.1923
R_work r_work	0.1900
R_free r_free	0.2367

Crystal structure of the OkaE-M71A mutant with a-ketoglutarate and okaramine A

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

Iron/alpha-ketoglutarate-dependent dioxygenase okaE

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

9uag__assembly_1__model_1

9uag__assembly_1__model_1 | I(q)

9uag__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 the OkaE-M71A mutant with a-ketoglutarate and okaramine A

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

Iron/alpha-ketoglutarate-dependent dioxygenase okaE

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

9uag__assembly_1__model_1

9uag__assembly_1__model_1 | I(q)

9uag__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)