SAXSdb — 9ryg

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

Decarboxylase NovR

Streptomyces niveus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	3-(3-methylbut-2-enyl)-4-oxidanyl-benzoic acid × 4 FE (III) ION × 4 SULFATE ION × 6 1,2-ETHANEDIOL × 15 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOVR_STRNV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–275； UniProt 1–270 Author chain B； PDBConstruct 6–275； UniProt 1–270 Author chain C； PDBConstruct 6–275； UniProt 1–270 Author chain D； PDBConstruct 6–275； UniProt 1–270

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	9ryg
Deposition date deposition_date	2025-07-15
Last revision last_revision	2025-07-23
Structure title title	Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound
Keywords keywords	homotetramer, C4 symmetry, 3-dimethylallyl-4-hydroxybenzoate, LYASE; LYASE
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.

9ryg__assembly_1__model_1

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

Download this curve (.dat)

9ryg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ryg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.20 Å
Rg (electron density)	28.89 Å
Total Rg	29.70 Å
Atom count	8267
Residues	1030
Excluded volume	145510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ryg__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 (6)

Entity 1 Entity 1 polymer

Description description	Decarboxylase NovR
Molecular weight formula_weight	30562.4 kDa
EC 编号 ec_number	4.1.-.-
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	9253

DHPFTMSEALANMPGDDYFRQPPVFDTYAEHRAYLKFRHAVALRHFARLGFDQDGLAGLITVADPEHADTYWANPLAHPFSTITPADLIRVDGDSAETVEGQRRVNIAAFNIHAEIHRARPDVQAVIHLHTVYGRAFSAFARKLPPLTQDACPFFEDHEVFDDFTGLVLAKDDGRRIAKQLRGHKAILLKNHGLVTVGETLDAAAWWFTLLDTCCHVQLLADAAGKPEEIPAEVARLTGRQLGSHLLGWNSYQPLHEAALARDPDLATMEPALPS

Source Source

Source organism organism	Streptomyces niveus
NCBI taxonomy ID ncbi_taxonomy_id	193462
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	3-(3-methylbut-2-enyl)-4-oxidanyl-benzoic acid
Molecular weight formula_weight	206.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	883

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Unit-cell length a length_a	86.508 Å
Unit-cell length b length_b	138.968 Å
Unit-cell length c length_c	100.615 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.791 Å
Low-resolution limit resolution_low	49.356 Å
R factor r_factor	—
R_work r_work	0.1608
R_free r_free	0.1883

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

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

Decarboxylase NovR

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

9ryg__assembly_1__model_1

9ryg__assembly_1__model_1 | I(q)

9ryg__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

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

Decarboxylase NovR

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

9ryg__assembly_1__model_1

9ryg__assembly_1__model_1 | I(q)

9ryg__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)