SAXSdb — 1dj9

▼

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

8-AMINO-7-OXONONANOATE SYNTHASE

OrganismNot specified

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 1–384	Not recorded	SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 KAM N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K	Resolution 2.00 Å R-free 0.278
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–384	Not recorded	SO4 SULFATE ION × 4 MG MAGNESIUM ION × 2 KAM N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K	Resolution 2.00 Å R-free 0.278

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 1DJ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BS0 PLP-DEPENDENT ACYL-COA SYNTHASE Deposited 1998-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–384（384 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.9；PROTEIN WAS CRYSTALLIZED FROM 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS,, pH 7.9	Resolution 1.65 Å R-free 0.212
1BS0 PLP-DEPENDENT ACYL-COA SYNTHASE Deposited 1998-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–384（384 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.9；PROTEIN WAS CRYSTALLIZED FROM 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS,, pH 7.9	Resolution 1.65 Å R-free 0.212
1DJE CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF 8-AMINO-7-OXONANOATE SYNTHASE Deposited 1999-12-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–384（384 aa）	Not recorded	SO4 SULFATE ION × 3 PLP PYRIDOXAL-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUN CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.71 Å R-free 0.245
1DJE CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF 8-AMINO-7-OXONANOATE SYNTHASE Deposited 1999-12-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–384（384 aa）	Not recorded	SO4 SULFATE ION × 6 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUN CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.71 Å R-free 0.245
2G6W Suicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine Deposited 2006-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–384（384 aa）	Not recorded	LLF (4-{(E)-[(2,2-DIFLUOROETHYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；298 K；0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS, pH 7.0, EVAPORATION, temperature 298K	Resolution 2.14 Å R-free 0.246

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

View Construct and Data Evidence

UniProt name	BIOF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–384； UniProt 1–384

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dj9
Deposition date deposition_date	1999-12-02
Structure title title	CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.
Keywords keywords	;8-AMINO-7-OXONONANOATE SYNTHASE, BIOTIN, PYRIDOXAL-5'-PHOSPHATE, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.53 Å
Radius of gyration Rg (electron density) rg_electron	21.35 Å
Forward intensity I(0) i0	32081600.00
Molecular weight molecular_weight	41994.0 kDa
Excluded volume excluded_volume	52009 Å³
Envelope volume envelope_volume	62848 Å³
Hydration-shell volume shell_volume	24258 Å³
Envelope diameter envelope_diameter	68.1 Å
Shell Rg shell_rg	28.33 Å
Envelope Rg envelope_rg	21.46 Å
Shape Rg shape_rg	21.36 Å
Total Rg total_rg	22.17 Å
Total atoms total_atoms	2951
Residues n_residues	383
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.6 Å
Rg (real space) rg_real	22.40 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	3.2080e+07
I(0) uncertainty (real space) i0_real_error	4.3520e+05
Rg (reciprocal space) rg_reciprocal	22.43 Å
I(0) (reciprocal space) i0_reciprocal	32080000.0000
Solution quality estimate total_estimate	0.9120
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.603
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5774000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.973

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	8-AMINO-7-OXONONANOATE SYNTHASE
Molecular weight formula_weight	41539.1 kDa
EC 编号 ec_number	2.3.1.47
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3288

MSWQEKINAALDARGAADALRRRYPVAQGAGRWLVADDRQYLNFSSNDYLGLSHHPQIIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIAAMMAKEDRIAADRLSHASLLEAASLSPSQLRRFAHNDVTHLARLLASPCPGQQMVVTEGVFSMDGDSAPLAEIQQVTQQHNGWLMVDDAHGTGVIGEQGRGSCWLQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHLIYSTSMPPAQAQALRASLAVIRSDEGDARREKLAALITRFRAGVQDLPFTLADSCSAIQPLIVGDNSRALQLAEKLRQQGCWVTGIRPPTVPAGIARLRLTLTAAHEMQDIDRLLEVLHGNG

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
Molecular weight formula_weight	418.4 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	337

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dj9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1dj9A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1dj9A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

8. Citations (2)

▶

Unit-cell length a length_a	58.890 Å
Unit-cell length b length_b	58.890 Å
Unit-cell length c length_c	201.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2780

fit	/app/data/saxs_computation/dj/1dj9/1dj9.fit
pddf	/app/data/pr_computation/dj/1dj9/1dj9.pr.out
profile	/app/data/saxs_computation/dj/1dj9/1dj9.dat

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

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

8-AMINO-7-OXONONANOATE SYNTHASE

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