SAXSdb — 2bkj

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

FLAVIN REDUCTASE

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–240 Chain B； UniProt 1–240	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.08 Å R-free 0.206

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 2BKJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BKJ NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI Deposited 1998-07-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–240（240 aa） Chain B 1–240（240 aa）	Not recorded	PO4 PHOSPHATE ION × 2 FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.80 Å R-free 0.207

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FRP_VIBHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240 Author chain B； PDBConstruct 1–240； UniProt 1–240

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	2bkj
Deposition date deposition_date	1998-07-23
Structure title title	NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI COMPLEXED WITH NAD+
Keywords keywords	OXIDOREDUCTASE, FRP; 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	21.81 Å
Radius of gyration Rg (electron density) rg_electron	20.56 Å
Forward intensity I(0) i0	42804000.00
Molecular weight molecular_weight	49849.0 kDa
Excluded volume excluded_volume	61934 Å³
Envelope volume envelope_volume	69674 Å³
Hydration-shell volume shell_volume	27015 Å³
Envelope diameter envelope_diameter	68.1 Å
Shell Rg shell_rg	28.38 Å
Envelope Rg envelope_rg	20.72 Å
Shape Rg shape_rg	20.59 Å
Total Rg total_rg	21.30 Å
Total atoms total_atoms	3502
Residues n_residues	460
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	65.6 Å
Rg (real space) rg_real	21.60 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	4.2800e+07
I(0) uncertainty (real space) i0_real_error	5.1780e+05
Rg (reciprocal space) rg_reciprocal	21.64 Å
I(0) (reciprocal space) i0_reciprocal	42800000.0000
Solution quality estimate total_estimate	0.8998
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.048
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15550000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.995

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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	FLAVIN REDUCTASE
Molecular weight formula_weight	26333.6 kDa
EC 编号 ec_number	1.6.99.-
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	3575

MNNTIETILAHRSIRKFTAVPITDEQRQTIIQAGLAASSSSMLQVVSIVRVTDSEKRNELAQFAGNQAYVESAAEFLVFCIDYQRHATINPDVQADFTELTLIGAVDSGIMAQNCLLAAESMGLGGVYIGGLRNSAAQVDELLGLPENSAVLFGMCLGHPDQNPEVKPRLPAHVVVHENQYQELNLDDIQSYDQTMQAYYASRTSNQKLSTWSQEVTGKLAGESRPHILPYLNSKGLAKR

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 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 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 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	73

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bkja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.1 — NADH oxidase/flavin reductase

Domain ID domain_id	d2bkjb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.1 — NADH oxidase/flavin reductase

CATH v4.4 (2 domains)

Domain ID domain_id	2bkjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

Domain ID domain_id	2bkjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

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8. Citations (3)

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Unit-cell length a length_a	51.200 Å
Unit-cell length b length_b	85.900 Å
Unit-cell length c length_c	59.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.70 °
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	2.080 Å
Low-resolution limit resolution_low	32.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2060

fit	/app/data/saxs_computation/bk/2bkj/2bkj.fit
pddf	/app/data/pr_computation/bk/2bkj/2bkj.pr.out
profile	/app/data/saxs_computation/bk/2bkj/2bkj.dat

NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI COMPLEXED WITH NAD+

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

FLAVIN REDUCTASE

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