SAXSdb — 1axj

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

FMN-BINDING PROTEIN

;Desulfovibrio vulgaris str. 'Miyazaki F' ;

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 1–122	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	SOLUTION NMR NMR measurement conditions：pH 6.8；309 K	Resolution not provided

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 1AXJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLM DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) Deposited 1999-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% PEG6000, 0.1M TRIS(PH7.5), 20% GRYCEROL, 0.2M NACL	Resolution 1.30 Å R-free 0.182
1WLI L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2004-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：L122Y Mutation：L122Y	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.185
1WLK L122E mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2004-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：L122E Mutation：L122E	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG6000, sodium acetate, Tris , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
1WLK L122E mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2004-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–122（122 aa） Chain D 1–122（122 aa）	Mutation：L122E Mutation：L122E	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG6000, sodium acetate, Tris , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
2E83 T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2007-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：T31V Mutation：T31V	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；PEG 6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.52 Å R-free 0.188
3A20 L122K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2009-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：L122K Mutation：L122K	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG 6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.188
3A6Q E13T mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：E13T Mutation：E13T	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.40 Å R-free 0.182
3A6R E13Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：E13Q Mutation：E13Q	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.20 Å R-free 0.189
3A6R E13Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–122（122 aa） Chain D 1–122（122 aa）	Mutation：E13Q Mutation：E13Q	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.20 Å R-free 0.189
3AMF E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2010-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：E13R Mutation：E13R	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；22% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.60 Å R-free 0.224
3AWH E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2011-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：E13K Mutation：E13K	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.60 Å R-free 0.207
3VY2 N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2012-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：N33D Mutation：N33D	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；23% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.60 Å R-free 0.192
3VY5 N33Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2012-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：N33Q Mutation：N33Q	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 16.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.40 Å R-free 0.184
3VYA W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2012-09-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa）	Mutation：W32Y	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.05；293 K；100mM HEPES, 85%(v/v) 2-Methyl-2,4-pentanediol, 50%(w/v) polyethylene glycol 400, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.273

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FMNB_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 1–122

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	1axj
Deposition date deposition_date	1997-10-16
Structure title title	FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F), NMR, 20 STRUCTURES
Keywords keywords	FMN-BINDING PROTEIN, BINDING PROTEIN; BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.19 Å
Radius of gyration Rg (electron density) rg_electron	13.75 Å
Forward intensity I(0) i0	1037020000.00
Molecular weight molecular_weight	271910.0 kDa
Excluded volume excluded_volume	339960 Å³
Envelope volume envelope_volume	24573 Å³
Hydration-shell volume shell_volume	13900 Å³
Envelope diameter envelope_diameter	48.9 Å
Shell Rg shell_rg	20.80 Å
Envelope Rg envelope_rg	15.18 Å
Shape Rg shape_rg	13.75 Å
Total Rg total_rg	13.87 Å
Total atoms total_atoms	38320
Residues n_residues	2440
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	41.8 Å
Rg (real space) rg_real	14.09 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.0370e+09
I(0) uncertainty (real space) i0_real_error	1.1180e+07
Rg (reciprocal space) rg_reciprocal	14.09 Å
I(0) (reciprocal space) i0_reciprocal	1037000000.0000
Solution quality estimate total_estimate	0.9079
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	183300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.885

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1axja_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

CATH v4.4 (1 domains)

Domain ID domain_id	1axjA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	FMN-BINDING PROTEIN
Molecular weight formula_weight	13153.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	38320

来源生物 organism	;Desulfovibrio vulgaris str. 'Miyazaki F' ;
NCBI Class编号 ncbi_taxonomy_id	883
宿主生物 host_organism	Escherichia coli

FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F), NMR, 20 STRUCTURES

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

FMN-BINDING PROTEIN

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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/ax/1axj/1axj.fit
pddf	/app/data/pr_computation/ax/1axj/1axj.pr.out
profile	/app/data/saxs_computation/ax/1axj/1axj.dat