SAXSdb — 3fgc

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

Alkanal monooxygenase alpha chain

Vibrio harveyi

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–355	Not recorded	Alkanal monooxygenase beta chain × 1 （P07739） FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–355	Not recorded	Alkanal monooxygenase beta chain × 1 （P07739） PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.241

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 3FGC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–355（355 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1LUC BACTERIAL LUCIFERASE Deposited 1996-05-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa）	Not recorded	MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LUXA_VIBHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain C； PDBConstruct 1–355； UniProt 1–355

Alkanal monooxygenase beta chain

Vibrio harveyi

UniProt P07739

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–324	Not recorded	Alkanal monooxygenase alpha chain × 1 （P07740） FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–324	Not recorded	Alkanal monooxygenase alpha chain × 1 （P07740） PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.241

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 3FGC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–324（324 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–324（324 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1BSL STRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN Deposited 1996-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–324（324 aa） Fragment：BETA SUBUNIT Chain B 1–324（324 aa） Fragment：BETA SUBUNIT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å
1LUC BACTERIAL LUCIFERASE Deposited 1996-05-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–324（324 aa）	Not recorded	MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1XKJ BACTERIAL LUCIFERASE BETA2 HOMODIMER Deposited 1996-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–324（324 aa） Chain B 1–324（324 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；SITTING DROP, 277 KELVIN, 12% PEG 4000, 17-21% ISOPROPANOL, 0.006M DTT, 0.1M CITRATE PH 6.2. 50 MG/ML PROTEIN., vapor diffusion - sitting drop	Resolution 2.50 Å R-free 0.249

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LUXB_VIBHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–324； UniProt 1–324 Author chain D； PDBConstruct 1–324； UniProt 1–324

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	3fgc
Deposition date deposition_date	2008-12-05
Structure title title	Crystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication
Keywords keywords	FMN bacterial luciferase mobile loop, Flavoprotein, FMN, Luminescence, Monooxygenase, Oxidoreductase, Photoprotein; 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	41.41 Å
Radius of gyration Rg (electron density) rg_electron	41.47 Å
Forward intensity I(0) i0	372588000.00
Molecular weight molecular_weight	152740.0 kDa
Excluded volume excluded_volume	188500 Å³
Envelope volume envelope_volume	242340 Å³
Hydration-shell volume shell_volume	50752 Å³
Envelope diameter envelope_diameter	148.7 Å
Shell Rg shell_rg	44.37 Å
Envelope Rg envelope_rg	41.29 Å
Shape Rg shape_rg	41.46 Å
Total Rg total_rg	41.66 Å
Total atoms total_atoms	10724
Residues n_residues	1339
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	138.8 Å
Rg (real space) rg_real	41.70 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	3.7260e+08
I(0) uncertainty (real space) i0_real_error	6.6900e+06
Rg (reciprocal space) rg_reciprocal	41.41 Å
I(0) (reciprocal space) i0_reciprocal	372500000.0000
Solution quality estimate total_estimate	0.8201
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.5 Å
Skewness Skewness skewness	0.503
Kurtosis Kurtosis kurtosis	-0.457
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	142900000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.508

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Alkanal monooxygenase alpha chain
Molecular weight formula_weight	40197.1 kDa
EC 编号 ec_number	1.14.14.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11895

MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQWRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ

来源 Source

来源生物 organism	Vibrio harveyi
NCBI Class编号 ncbi_taxonomy_id	669
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Alkanal monooxygenase beta chain
Molecular weight formula_weight	37455.8 kDa
EC 编号 ec_number	1.14.14.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MKFGLFFLNFMNSKRSSDQVIEEMLDTAHYVDQLKFDTLAVYENHFSNNGVVGAPLTVAGFLLGMTKNAKVASLNHVITTHHPVRVAEEACLLDQMSEGRFAFGFSDCEKSADMRFFNRPTDSQFQLFSECHKIINDAFTTGYCHPNNDFYSFPKISVNPHAFTEGGPAQFVNATSKEVVEWAAKLGLPLVFRWDDSNAQRKEYAGLYHEVAQAHGVDVSQVRHKLTLLVNQNVDGEAARAEARVYLEEFVRESYSNTDFEQKMGELLSENAIGTYEESTQAARVAIECCGAADLLMSFESMEDKAQQRAVIDVVNANIVKYHSLEHHHHHH

来源 Source

来源生物 organism	Vibrio harveyi
NCBI Class编号 ncbi_taxonomy_id	669
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	781

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3fgca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.1 — Bacterial luciferase (alkanal monooxygenase)

Domain ID domain_id	d3fgcb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.1 — Bacterial luciferase (alkanal monooxygenase)

Domain ID domain_id	d3fgcc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.1 — Bacterial luciferase (alkanal monooxygenase)

Domain ID domain_id	d3fgcd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.1 — Bacterial luciferase (alkanal monooxygenase)

Domain ID domain_id	d3fgcd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3fgcA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3fgcB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3fgcC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3fgcD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

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8. Citations (1)

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Unit-cell length a length_a	58.886 Å
Unit-cell length b length_b	109.301 Å
Unit-cell length c length_c	301.419 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	27.330 Å
R factor r_factor	0.1867
R_work r_work	0.1839
R_free r_free	0.2409

fit	/app/data/saxs_computation/fg/3fgc/3fgc.fit
pddf	/app/data/pr_computation/fg/3fgc/3fgc.pr.out
profile	/app/data/saxs_computation/fg/3fgc/3fgc.dat

Crystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication

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

Alkanal monooxygenase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Alkanal monooxygenase beta chain

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)