SAXSdb — 5kyt

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

Luciferin 4-monooxygenase

Photinus pyralis

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–550	Mutation：S284T	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；23 % PEG 8000, 300 mM Na/K tartrate, 1.00 mM Tris	Resolution 2.00 Å R-free 0.218
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–550	Mutation：S284T	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；23 % PEG 8000, 300 mM Na/K tartrate, 1.00 mM Tris	Resolution 2.00 Å R-free 0.218

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 5KYT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BA3 FIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM Deposited 1998-04-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	MBR TRIBROMOMETHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 7.8；283 K；2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL., microbatch under oil, temperature 283K	Resolution 2.20 Å R-free 0.239
1LCI FIREFLY LUCIFERASE Deposited 1996-06-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 7.8；283 K；2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL. CRYOPROTECTANT SOLUTION: 8% PEG 8000, 10% GLYCEROL, 12.5% ETHYLENE GLYCOL, 0.1M TRIS-HCL PH7.8, microbatch under oil, temperature 283K	Resolution 2.00 Å R-free 0.265
3IEP Firefly luciferase apo structure (P41 form) Deposited 2009-07-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% PEG 1500, 8% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.221
3IER Firefly luciferase apo structure (P41 form) with PEG 400 bound Deposited 2009-07-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25% PEG 400, 20% PEG 3350, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.05 Å R-free 0.225
3IES Firefly luciferase inhibitor complex Deposited 2009-07-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	M24 5'-O-[(R)-[({3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]phenyl}carbonyl)oxy](hydroxy)phosphoryl]adenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% PEG 1500, 8% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.00 Å R-free 0.218
3RIX 1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex Deposited 2011-04-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	923 (5Z)-4-hydroxy-3-[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]-5-{[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]methylidene}furan-2(5H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25% (v/v) PEG 400, 20% (v/v) PEG 3350, 0.1 M MgCl2, 0.1 M Tris, pH 8.5, vapor diffusion, temperature 277K	Resolution 1.70 Å R-free 0.218
4E5D 2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex Deposited 2012-03-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	0NJ 2-(2-fluorophenyl)-6-methoxy-1,3-benzothiazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25% (v/v) PEG 400, 20% (v/v) PEG 3350, 0.1 M MgCl2, 0.1 M Tris, pH 8.5, vapor diffusion, temperature 277K	Resolution 2.20 Å R-free 0.232
4G36 Photinus pyralis luciferase in the adenylate-forming conformation bound to DLSA Deposited 2012-07-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；300 mM Na/K Tartrate, 20% PEG 6000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.238
4G36 Photinus pyralis luciferase in the adenylate-forming conformation bound to DLSA Deposited 2012-07-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–550（550 aa）	Not recorded	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；300 mM Na/K Tartrate, 20% PEG 6000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.238
4G37 Structure of cross-linked firefly luciferase in second catalytic conformation Deposited 2012-07-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Mutation：C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 XLX 4,4'-(ethylenediimino)bis[4-oxobutyrate] × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.40 Å R-free 0.259
4G37 Structure of cross-linked firefly luciferase in second catalytic conformation Deposited 2012-07-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–550（550 aa）	Mutation：C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 XLX 4,4'-(ethylenediimino)bis[4-oxobutyrate] × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.40 Å R-free 0.259
5DV9 Crystal structure of the Luciferase Deposited 2015-09-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；Li2SO4, PEG 8000, Tris	Resolution 2.40 Å R-free 0.241
5DWV Crystal structure of the Luciferase complexed with substrate analogue Deposited 2015-09-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	5J4 2-[6-(cyclobuta-1,3-dien-1-ylamino)-1,3-benzothiazol-2-yl]-1,3-thiazol-4-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；Li2SO4, PEG8000, Tris	Resolution 2.30 Å R-free 0.228
5GYZ luciferase AMP/7-cy-L complex Deposited 2016-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–438（435 aa） Fragment：UNP residues 4-438	Not recorded	7BV (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；Sodium malonate, PEG3350	Resolution 2.40 Å R-free 0.227
5GZ2 luciferase complex with 7-cy-L Deposited 2016-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–438（436 aa） Fragment：UNP residues 3-438	Not recorded	7BV (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；Sodium malonate , PEG3350	Resolution 2.00 Å R-free 0.239
5KYV Structure of Photinus pyralis Luciferase green shifted light emitting variant Deposited 2016-07-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Mutation：V241I, G246A, F250S	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；23 % PEG 8000, 200 mM Na/K tartrate, 1.00 mM Tris	Resolution 2.50 Å R-free 0.247
5KYV Structure of Photinus pyralis Luciferase green shifted light emitting variant Deposited 2016-07-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–550（550 aa）	Mutation：V241I, G246A, F250S	SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；23 % PEG 8000, 200 mM Na/K tartrate, 1.00 mM Tris	Resolution 2.50 Å R-free 0.247
5WYS luciferase with inhibitor 3i Deposited 2017-01-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Not recorded	7V6 5-[(3R)-3-(4-boranylphenyl)-3-oxidanyl-propyl]-2-oxidanyl-benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；293 K；0.5 M Li2SO4, 15% PEG8000, 0.1 M Tris	Resolution 3.00 Å R-free 0.270
6HPS Near-infrared dual bioluminescence imaging in vivo using infra-luciferin Deposited 2018-09-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–546（543 aa）	Not recorded	GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000	Resolution 3.10 Å R-free 0.333
6HPS Near-infrared dual bioluminescence imaging in vivo using infra-luciferin Deposited 2018-09-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–546（543 aa）	Not recorded	GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000	Resolution 3.10 Å R-free 0.333
6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–550（550 aa）	Mutation：T214N, A222C, Y255F, S276T, H332N, E354N	SO4 SULFATE ION × 1 DYD (2S,5S)-hexane-2,5-diol × 2 EDO 1,2-ETHANEDIOL × 16 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol	Resolution 2.75 Å R-free 0.218
6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–550（550 aa）	Mutation：T214N, A222C, Y255F, S276T, H332N, E354N	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 7 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol	Resolution 2.75 Å R-free 0.218
6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–550（550 aa）	Mutation：T214N, A222C, Y255F, S276T, H332N, E354N	SO4 SULFATE ION × 2 DYD (2S,5S)-hexane-2,5-diol × 2 EDO 1,2-ETHANEDIOL × 16 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol	Resolution 2.75 Å R-free 0.218

17 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LUCI_PHOPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–550； UniProt 1–550 Author chain B； PDBConstruct 1–550； UniProt 1–550

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	5kyt
Deposition date deposition_date	2016-07-22
Structure title title	Structure of Photinus pyralis Luciferase red light emitting variant
Keywords keywords	adenylation forming enzyme, ligase, OXIDOREDUCTASE; OXIDOREDUCTASE
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	34.00 Å
Radius of gyration Rg (electron density) rg_electron	33.50 Å
Forward intensity I(0) i0	200766000.00
Molecular weight molecular_weight	117800.0 kDa
Excluded volume excluded_volume	148960 Å³
Envelope volume envelope_volume	184720 Å³
Hydration-shell volume shell_volume	45519 Å³
Envelope diameter envelope_diameter	117.2 Å
Shell Rg shell_rg	40.27 Å
Envelope Rg envelope_rg	33.74 Å
Shape Rg shape_rg	33.48 Å
Total Rg total_rg	34.08 Å
Total atoms total_atoms	8308
Residues n_residues	1075
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	109.5 Å
Rg (real space) rg_real	34.00 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.0080e+08
I(0) uncertainty (real space) i0_real_error	3.2390e+06
Rg (reciprocal space) rg_reciprocal	34.00 Å
I(0) (reciprocal space) i0_reciprocal	200800000.0000
Solution quality estimate total_estimate	0.8932
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.3 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52430000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.879

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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	Luciferin 4-monooxygenase
Molecular weight formula_weight	60833.0 kDa
EC 编号 ec_number	1.13.12.7
Mutation mutation	S284T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9046

MEDAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQTALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIKAKKGGKSKL

来源 Source

来源生物 organism	Photinus pyralis
通用名 common_name	Common eastern firefly
NCBI Class编号 ncbi_taxonomy_id	7054
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 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	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	698

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5kyta_
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

Domain ID domain_id	d5kytb_
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 (6 domains)

Domain ID domain_id	5kytA01
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	5kytA02
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	5kytA03
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	5kytB01
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	5kytB02
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	5kytB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	980 —

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8. Citations (1)

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Unit-cell length a length_a	92.587 Å
Unit-cell length b length_b	92.587 Å
Unit-cell length c length_c	294.465 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.001 Å
Low-resolution limit resolution_low	33.452 Å
R factor r_factor	0.1803
R_work r_work	0.1782
R_free r_free	0.2183

fit	/app/data/saxs_computation/ky/5kyt/5kyt.fit
pddf	/app/data/pr_computation/ky/5kyt/5kyt.pr.out
profile	/app/data/saxs_computation/ky/5kyt/5kyt.dat

Structure of Photinus pyralis Luciferase red light emitting variant

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

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