SAXSdb — 9yl5

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–155 Chain B； UniProt 1–155 Chain C； UniProt 1–155 Chain D； UniProt 1–155 Chain E； UniProt 1–155	Not recorded	CL CHLORIDE ION × 36 LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Morpheus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 2mM ligand added to protein prior to crystallization. plate 19802 B9 drop 1, Puck: PSL-2810, Cryo: direct	Resolution 2.56 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YL5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZNH Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis Deposited 2025-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–155（155 aa） Fragment：residues 1-155 Chain B 1–155（155 aa） Fragment：residues 1-155 Chain C 1–155（155 aa） Fragment：residues 1-155 Chain D 1–155（155 aa） Fragment：residues 1-155 Chain E 1–155（155 aa） Fragment：residues 1-155	Not recorded	CL CHLORIDE ION × 6 PG4 TETRAETHYLENE GLYCOL × 4 BCN BICINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Morpheus E12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. The diffraction data where highly ansiotropic resulting in high B-factors. Therefore the anisotropically truncated data (staraniso) were used for refinement and both data sets were deposited. plate 19802 E12 drop 1, Puck: PSL-1009, Cryo: direct	Resolution 2.34 Å R-free 0.259
9ZNJ Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 6,7-dimethyl-8-(1'-D-ribityl) lumazine Deposited 2025-12-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–155（155 aa） Fragment：residues 1-155 Chain B 1–155（155 aa） Fragment：residues 1-155 Chain C 1–155（155 aa） Fragment：residues 1-155 Chain D 1–155（155 aa） Fragment：residues 1-155 Chain E 1–155（155 aa） Fragment：residues 1-155	Not recorded	PO4 PHOSPHATE ION × 12 CL CHLORIDE ION × 32 DLZ 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 24 hour soak with 2 mM 6,7-dimethyl-8-(1'-D-ribityl) lumazine. plate 19802 B12, Puck: PSL-0104, Cryo: direct	Resolution 2.15 Å R-free 0.261

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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	9yl5
Deposition date deposition_date	2025-10-08
最后修订 last_revision	2025-10-22
Structure title title	Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.20 Å
Radius of gyration Rg (electron density) rg_electron	26.06 Å
Forward intensity I(0) i0	111583000.00
Molecular weight molecular_weight	80548.0 kDa
Excluded volume excluded_volume	99755 Å³
Envelope volume envelope_volume	118150 Å³
Hydration-shell volume shell_volume	36350 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	34.56 Å
Envelope Rg envelope_rg	26.11 Å
Shape Rg shape_rg	26.06 Å
Total Rg total_rg	26.85 Å
Total atoms total_atoms	5621
Residues n_residues	765
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.0 Å
Rg (real space) rg_real	27.04 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.1160e+08
I(0) uncertainty (real space) i0_real_error	1.6970e+06
Rg (reciprocal space) rg_reciprocal	27.09 Å
I(0) (reciprocal space) i0_reciprocal	111600000.0000
Solution quality estimate total_estimate	0.9093
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.524
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30550000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.937

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	5652

MAHHHHHHMNPYILTPDLNGEGLHIGIVRARFNEEIGQAQLQACLEELGKLGVDERDVMVVSVPGALELGVALARMAESYEFDALIALGAVIRGETYHFEVVSNESAAAISRIALETGIPVANGVLTVDTDEQAQARAAGKGADCAQVAVEMANLAAALEPEE

来源 Source

来源生物 organism	Bordetella pertussis Tohama I
NCBI Class编号 ncbi_taxonomy_id	257313
宿主生物 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	18

Entity 3 Entity 3 non-polymer

Description description	5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
Molecular weight formula_weight	290.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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8. Citations (1)

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Unit-cell length a length_a	97.126 Å
Unit-cell length b length_b	75.061 Å
Unit-cell length c length_c	180.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.560 Å
Low-resolution limit resolution_low	74.430 Å
R factor r_factor	0.2033
R_work r_work	0.2010
R_free r_free	0.2485

fit	/app/data/saxs_computation/yl/9yl5/9yl5.fit
pddf	/app/data/pr_computation/yl/9yl5/9yl5.pr.out
profile	/app/data/saxs_computation/yl/9yl5/9yl5.dat

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction