1c41

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: 152.4 Å Quality: REASONABLE

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

LUMAZINE SYNTHASE

Magnaporthe grisea

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–200 Chain B； UniProt 1–200 Chain C； UniProt 1–200 Chain D； UniProt 1–200 Chain E； UniProt 1–200	Not recorded	SO4 SULFATE ION × 10 LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 3.10 Å R-free 0.271
2	Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain F； UniProt 1–200 Chain G； UniProt 1–200 Chain H； UniProt 1–200 Chain I； UniProt 1–200 Chain J； UniProt 1–200	Not recorded	SO4 SULFATE ION × 10 LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 3.10 Å R-free 0.271
3	Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–200 Chain B； UniProt 1–200 Chain C； UniProt 1–200 Chain D； UniProt 1–200 Chain E； UniProt 1–200 Chain F； UniProt 1–200 Chain G； UniProt 1–200 Chain H； UniProt 1–200 Chain I； UniProt 1–200 Chain J； UniProt 1–200	Not recorded	SO4 SULFATE ION × 20 LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 10	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 3.10 Å R-free 0.271

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	RIB4_MAGGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 1–200 Author chain B； PDBConstruct 1–200； UniProt 1–200 Author chain C； PDBConstruct 1–200； UniProt 1–200 Author chain D； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain F； PDBConstruct 1–200； UniProt 1–200 Author chain G； PDBConstruct 1–200； UniProt 1–200 Author chain H； PDBConstruct 1–200； UniProt 1–200 Author chain I； PDBConstruct 1–200； UniProt 1–200 Author chain J； PDBConstruct 1–200； UniProt 1–200

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	1c41
Deposition date deposition_date	1999-08-03
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	50.84 Å
Radius of gyration Rg (electron density) rg_electron	50.86 Å
Forward intensity I(0) i0	487971000.00
Molecular weight molecular_weight	181190.0 kDa
Excluded volume excluded_volume	225400 Å³
Envelope volume envelope_volume	296340 Å³
Hydration-shell volume shell_volume	47258 Å³
Envelope diameter envelope_diameter	167.8 Å
Shell Rg shell_rg	57.25 Å
Envelope Rg envelope_rg	49.32 Å
Shape Rg shape_rg	50.85 Å
Total Rg total_rg	51.08 Å
Total atoms total_atoms	12730
Residues n_residues	1650
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	152.4 Å
Rg (real space) rg_real	51.12 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	4.8800e+08
I(0) uncertainty (real space) i0_real_error	9.1670e+06
Rg (reciprocal space) rg_reciprocal	50.58 Å
I(0) (reciprocal space) i0_reciprocal	487600000.0000
Solution quality estimate total_estimate	0.6819
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-1.069
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48700000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.426; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.579; Smooth: 0.003

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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	LUMAZINE SYNTHASE
Molecular weight formula_weight	21093.9 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	12740

MHTKGPTPQQHDGSALRIGIVHARWNETIIEPLLAGTKAKLLACGVKESNIVVQSVPGSWELPIAVQRLYSASQLQTPSSGPSLSAGDLLGSSTTDLTALPTTTASSTGPFDALIAIGVLIKGETMHFEYIADSVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKARAGVIEGSHNHGEDWGLAAVEMGVRRRDWAAGKTE

来源 Source

来源生物 organism	Magnaporthe grisea
NCBI Class编号 ncbi_taxonomy_id	148305
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

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	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1c41a_
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	d1c41b_
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	d1c41c_
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	d1c41d_
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	d1c41e_
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	d1c41f_
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	d1c41g_
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	d1c41h_
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	d1c41i_
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	d1c41j_
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 (10 domains)

Domain ID domain_id	1c41A00
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	1c41B00
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	1c41C00
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	1c41D00
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	1c41E00
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	1c41F00
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	1c41G00
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	1c41H00
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	1c41I00
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	1c41J00
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	98.800 Å
Unit-cell length b length_b	124.700 Å
Unit-cell length c length_c	141.400 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	40

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.2710

fit	/app/data/saxs_computation/c4/1c41/1c41.fit
pddf	/app/data/pr_computation/c4/1c41/1c41.pr.out
profile	/app/data/saxs_computation/c4/1c41/1c41.dat