SAXSdb — 3vy2

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

FMN-binding protein

Desulfovibrio vulgaris

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–122 Chain B； UniProt 1–122	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

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 3VY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AXJ FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F), NMR, 20 STRUCTURES Deposited 1997-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–122（122 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	SOLUTION NMR NMR measurement conditions pH 6.8；309 K	Resolution not provided
1FLM DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) Deposited 1999-03-10	Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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
3VY5 N33Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Deposited 2012-09-21	Different mutation/modification Different ligand/ion 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 construct Different mutation/modification 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 Author chain B； 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	3vy2
Deposition date deposition_date	2012-09-21
Structure title title	N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Keywords keywords	Electron transport; ELECTRON TRANSPORT
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	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.25 Å
Forward intensity I(0) i0	13340500.00
Molecular weight molecular_weight	27191.0 kDa
Excluded volume excluded_volume	33989 Å³
Envelope volume envelope_volume	38228 Å³
Hydration-shell volume shell_volume	18337 Å³
Envelope diameter envelope_diameter	61.4 Å
Shell Rg shell_rg	23.73 Å
Envelope Rg envelope_rg	17.51 Å
Shape Rg shape_rg	17.27 Å
Total Rg total_rg	18.18 Å
Total atoms total_atoms	1914
Residues n_residues	244
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	64.4 Å
Rg (real space) rg_real	18.34 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.3340e+07
I(0) uncertainty (real space) i0_real_error	1.3860e+05
Rg (reciprocal space) rg_reciprocal	18.36 Å
I(0) (reciprocal space) i0_reciprocal	13340000.0000
Solution quality estimate total_estimate	0.8471
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.189
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4403000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	FMN-binding protein
Molecular weight formula_weight	13154.1 kDa
Mutation mutation	N33D
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	2149

MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWDSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL

来源 Source

来源生物 organism	Desulfovibrio vulgaris
NCBI Class编号 ncbi_taxonomy_id	883
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3vy2A00
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

Domain ID domain_id	3vy2B00
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	36.868 Å
Unit-cell length b length_b	83.038 Å
Unit-cell length c length_c	40.239 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1715
R_work r_work	0.1703
R_free r_free	0.1920

fit	/app/data/saxs_computation/vy/3vy2/3vy2.fit
pddf	/app/data/pr_computation/vy/3vy2/3vy2.pr.out
profile	/app/data/saxs_computation/vy/3vy2/3vy2.dat

N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

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

Refinement Refinement

Diffraction experiment Diffraction