SAXSdb — 2d1t

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

Luciferin 4-monooxygenase

Luciola cruciata

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 2 ;5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LUCI_LUCCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–548； UniProt 4–548

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	2d1t
Deposition date deposition_date	2005-08-31
Structure title title	Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue
Keywords keywords	ALPHA/BETA, BETA BARREL, ALPHA+BETA, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, Oxidoreductase; OXIDOREDUCTASE
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.

2d1t__assembly_1__model_1

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

Download this curve (.dat)

2d1t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d1t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.27 Å
Rg (electron density)	23.21 Å
Total Rg	24.15 Å
Atom count	4153
Residues	538
Excluded volume	74732 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d1t__assembly_1__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Luciferin 4-monooxygenase
Molecular weight formula_weight	60160.2 kDa
EC 编号 ec_number	1.13.12.7
Mutation mutation	T217I,S286N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5011

MENMENDENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYAEYLEKSCCLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAPTNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDSKVDYRGYQCLDTFIKRNTPPGYQASSFKTVEVDRKEQVALIMNSSGSTGLPKGVQLTHENIVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLGYLICGFRVVMLTKFDEETFLKTLQDYKCTNVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPEGDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAELESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILKKPVAKM

Source Source

Source organism organism	Luciola cruciata
Common name common_name	Japanese firefly
NCBI taxonomy ID ncbi_taxonomy_id	7051
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	;5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE ;
Molecular weight formula_weight	606.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	843

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2d1ta_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.1 — Acetyl-CoA synthetase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2d1tA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	38 — Luciferase; domain 3
Homologous superfamily homologous superfamily	10 — Luciferase; Domain 3

Domain ID domain_id	2d1tA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	980 —

Domain ID domain_id	2d1tA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	980 —

Domain ID domain_id	2d1tA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

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Unit-cell length a length_a	57.468 Å
Unit-cell length b length_b	181.174 Å
Unit-cell length c length_c	52.239 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	4

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

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1653
R_work r_work	0.1644
R_free r_free	0.1820

Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue

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

Luciferin 4-monooxygenase

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

2d1t__assembly_1__model_1

2d1t__assembly_1__model_1 | I(q)

2d1t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue

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

Luciferin 4-monooxygenase

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

2d1t__assembly_1__model_1

2d1t__assembly_1__model_1 | I(q)

2d1t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)