SAXSdb — 1knr

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

L-aspartate oxidase

Escherichia coli

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 1–540	Mutation：R386L	CL CHLORIDE ION × 1 NA SODIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；isopropanol, Hepes, sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.295

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 1KNR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CHU STRUCTURE OF L-ASPARTATE OXIDASE: IMPLICATIONS FOR THE SUCCINATE DEHYDROGENASE/ FUMARATE REDUCATSE FAMILY Deposited 1999-03-29	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 1–540（540 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；pH 8.3	Resolution 2.20 Å R-free 0.281
1KNP E. coli L-aspartate oxidase: mutant R386L in complex with succinate Deposited 2001-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：R386L	NA SODIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ispropanol, Hepes, sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	NADB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 1–540

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	1knr
Deposition date deposition_date	2001-12-19
Structure title title	L-aspartate oxidase: R386L mutant
Keywords keywords	succinate dehydrogenase, fumarate reductase family of oxidoreductases, 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	23.83 Å
Radius of gyration Rg (electron density) rg_electron	22.77 Å
Forward intensity I(0) i0	62370900.00
Molecular weight molecular_weight	59786.0 kDa
Excluded volume excluded_volume	74061 Å³
Envelope volume envelope_volume	85906 Å³
Hydration-shell volume shell_volume	30184 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	30.96 Å
Envelope Rg envelope_rg	23.17 Å
Shape Rg shape_rg	22.80 Å
Total Rg total_rg	23.58 Å
Total atoms total_atoms	4205
Residues n_residues	529
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	74.5 Å
Rg (real space) rg_real	23.69 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	6.2370e+07
I(0) uncertainty (real space) i0_real_error	7.9680e+05
Rg (reciprocal space) rg_reciprocal	23.73 Å
I(0) (reciprocal space) i0_reciprocal	62370000.0000
Solution quality estimate total_estimate	0.8201
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.203
Kurtosis Kurtosis kurtosis	-0.419
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19220000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L-aspartate oxidase
Molecular weight formula_weight	60386.3 kDa
EC 编号 ec_number	1.4.3.16
Mutation mutation	R386L
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4228

MNTLPEHSCDVLIIGSGAAGLSLALRLADQHQVIVLSKGPVTEGSTFYAQGGIAAVFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLFDTHIQPNGEESYHLTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRVLERTNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVVLATGGASKVYQYTTNPDISSGDGIAMAWRAGCRVANLEFNQFHPTALYHPQARNFLLTEALRGEGAYLKRPDGTRFMPDFDERGELAPRDIVARAIDHEMKRLGADCMFLDISHKPADFIRQHFPMIYEKLLGLGIDLTQEPVPIVPAAHYTCGGVMVDDHGRTDVEGLYAIGEVSYTGLHGANLMASNSLLECLVYGWSAAEDITRRMPYAHDISTLPPWDESRVENPDERVVIQHNWHELRLFMWDYVGIVRTTKRLERALRRITMLQQEIDEYYAHFRVSNNLLELRNLVQVAELIVRCAMMRKESRGLHFTLDYPELLTHSGPSILSPGNHYINR

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1knra1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
Family Family family	a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain

Domain ID domain_id	d1knra2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1knra3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	1knrA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1knrA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	1knrA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	100 — Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	73.278 Å
Unit-cell length b length_b	73.278 Å
Unit-cell length c length_c	313.933 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2521
R_work r_work	0.2498
R_free r_free	0.2954

fit	/app/data/saxs_computation/kn/1knr/1knr.fit
pddf	/app/data/pr_computation/kn/1knr/1knr.pr.out
profile	/app/data/saxs_computation/kn/1knr/1knr.dat

L-aspartate oxidase: R386L mutant

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

L-aspartate oxidase

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