1c2y

CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY

Method: X-RAY DIFFRACTION D_max: 156.4 Å Quality: GOOD

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

PROTEIN (LUMAZINE SYNTHASE)

Spinacia oleracea

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 67–222 Chain B； UniProt 67–222 Chain C； UniProt 67–222 Chain D； UniProt 67–222 Chain E； UniProt 67–222 Chain F； UniProt 67–222 Chain G； UniProt 67–222 Chain H； UniProt 67–222 Chain I； UniProt 67–222 Chain J； UniProt 67–222 Chain K； UniProt 67–222 Chain L； UniProt 67–222 Chain M； UniProt 67–222 Chain N； UniProt 67–222 Chain O； UniProt 67–222 Chain P； UniProt 67–222 Chain Q； UniProt 67–222 Chain R； UniProt 67–222 Chain S； UniProt 67–222 Chain T； UniProt 67–222	Not recorded	LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 20	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；0.1 M TRIS-HCL PH 7.6, 17 % PEG 1500, 5 % PEG 400, VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.326
2	Protein homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 67–222 Chain B； UniProt 67–222 Chain C； UniProt 67–222 Chain D； UniProt 67–222 Chain E； UniProt 67–222 Chain F； UniProt 67–222 Chain G； UniProt 67–222 Chain H； UniProt 67–222 Chain I； UniProt 67–222 Chain J； UniProt 67–222 Chain K； UniProt 67–222 Chain L； UniProt 67–222 Chain M； UniProt 67–222 Chain N； UniProt 67–222 Chain O； UniProt 67–222 Chain P； UniProt 67–222 Chain Q； UniProt 67–222 Chain R； UniProt 67–222 Chain S； UniProt 67–222 Chain T； UniProt 67–222	Not recorded	LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；0.1 M TRIS-HCL PH 7.6, 17 % PEG 1500, 5 % PEG 400, VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.326

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	RISB_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 67–222 Author chain B； PDBConstruct 1–156； UniProt 67–222 Author chain C； PDBConstruct 1–156； UniProt 67–222 Author chain D； PDBConstruct 1–156； UniProt 67–222 Author chain E； PDBConstruct 1–156； UniProt 67–222 Author chain F； PDBConstruct 1–156； UniProt 67–222 Author chain G； PDBConstruct 1–156； UniProt 67–222 Author chain H； PDBConstruct 1–156； UniProt 67–222 Author chain I； PDBConstruct 1–156； UniProt 67–222 Author chain J； PDBConstruct 1–156； UniProt 67–222 Author chain K； PDBConstruct 1–156； UniProt 67–222 Author chain L； PDBConstruct 1–156； UniProt 67–222 Author chain M； PDBConstruct 1–156； UniProt 67–222 Author chain N； PDBConstruct 1–156； UniProt 67–222 Author chain O； PDBConstruct 1–156； UniProt 67–222 Author chain P； PDBConstruct 1–156； UniProt 67–222 Author chain Q； PDBConstruct 1–156； UniProt 67–222 Author chain R； PDBConstruct 1–156； UniProt 67–222 Author chain S； PDBConstruct 1–156； UniProt 67–222 Author chain T； PDBConstruct 1–156； UniProt 67–222

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c2y
Deposition date deposition_date	1999-07-27
Structure title title	CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY
Keywords keywords	RIBOFLAVIN BIOSYNTHESIS, 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	49.20 Å
Radius of gyration Rg (electron density) rg_electron	49.15 Å
Forward intensity I(0) i0	1656890000.00
Molecular weight molecular_weight	334700.0 kDa
Excluded volume excluded_volume	416560 Å³
Envelope volume envelope_volume	535570 Å³
Hydration-shell volume shell_volume	88166 Å³
Envelope diameter envelope_diameter	158.0 Å
Shell Rg shell_rg	56.09 Å
Envelope Rg envelope_rg	47.83 Å
Shape Rg shape_rg	49.16 Å
Total Rg total_rg	49.29 Å
Total atoms total_atoms	23500
Residues n_residues	3100
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	156.4 Å
Rg (real space) rg_real	49.09 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.6570e+09
I(0) uncertainty (real space) i0_real_error	3.2690e+07
Rg (reciprocal space) rg_reciprocal	49.20 Å
I(0) (reciprocal space) i0_reciprocal	1657000000.0000
Solution quality estimate total_estimate	0.8347
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.6 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.583
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	267300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1c2ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2ye_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yi_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yj_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yk_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2ym_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yn_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yo_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yp_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yq_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yr_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2ys_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1c2yt_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

CATH v4.4 (20 domains)

Domain ID domain_id	1c2yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yO00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yP00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yQ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yR00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yS00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1c2yT00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

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8. Citations (1)

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Unit-cell length a length_a	218.240 Å
Unit-cell length b length_b	218.240 Å
Unit-cell length c length_c	218.240 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	240

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.3100
R_work r_work	0.3100
R_free r_free	0.3260

Description description	PROTEIN (LUMAZINE SYNTHASE)
Molecular weight formula_weight	16552.8 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	20

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Atom count atom_count	23500

CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY

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

PROTEIN (LUMAZINE 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Spinacia oleracea
通用名 common_name	spinach
NCBI Class编号 ncbi_taxonomy_id	3562
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	20

fit	/app/data/saxs_computation/c2/1c2y/1c2y.fit
pddf	/app/data/pr_computation/c2/1c2y/1c2y.pr.out
profile	/app/data/saxs_computation/c2/1c2y/1c2y.dat