SAXSdb — 9znh

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

6,7-dimethyl-8-ribityllumazine synthase

Bordetella pertussis Tohama I

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	CHLORIDE ION × 6 TETRAETHYLENE GLYCOL × 4 BICINE × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RISB_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–163； UniProt 1–155 Author chain B； PDBConstruct 9–163； UniProt 1–155 Author chain C； PDBConstruct 9–163； UniProt 1–155 Author chain D； PDBConstruct 9–163； UniProt 1–155 Author chain E； PDBConstruct 9–163； UniProt 1–155

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	9znh
Deposition date deposition_date	2025-12-12
Last revision last_revision	2025-12-24
Structure title title	Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, RIBOFLAVIN SYNTHASE, TRANSFERASE; TRANSFERASE
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.

9znh__assembly_1__model_1

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

Download this curve (.dat)

9znh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9znh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.13 Å
Rg (electron density)	25.94 Å
Total Rg	26.69 Å
Atom count	5406
Residues	760
Excluded volume	96052 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9znh__assembly_1__model_1`	pentameric （5）	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	6,7-dimethyl-8-ribityllumazine synthase
Molecular weight formula_weight	17318.5 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	5502

MAHHHHHHMNPYILTPDLNGEGLHIGIVRARFNEEIGQAQLQACLEELGKLGVDERDVMVVSVPGALELGVALARMAESYEFDALIALGAVIRGETYHFEVVSNESAAAISRIALETGIPVANGVLTVDTDEQAQARAAGKGADCAQVAVEMANLAAALEPEE

Source Source

Source organism organism	Bordetella pertussis Tohama I
NCBI taxonomy ID ncbi_taxonomy_id	257313
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	BICINE
Molecular weight formula_weight	163.2 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	96

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Unit-cell length a length_a	133.820 Å
Unit-cell length b length_b	75.050 Å
Unit-cell length c length_c	92.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.340 Å
Low-resolution limit resolution_low	46.730 Å
R factor r_factor	0.2166
R_work r_work	0.2144
R_free r_free	0.2594

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis

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

6,7-dimethyl-8-ribityllumazine 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

9znh__assembly_1__model_1

9znh__assembly_1__model_1 | I(q)

9znh__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 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis

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

6,7-dimethyl-8-ribityllumazine 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

9znh__assembly_1__model_1

9znh__assembly_1__model_1 | I(q)

9znh__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)