SAXSdb — 1a82

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

DETHIOBIOTIN SYNTHETASE

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–224	Not recorded	MG MAGNESIUM ION × 2 DNN 7,8-DIAMINO-NONANOIC ACID × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 1.80 Å R-free 0.246

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 1A82	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BS1 DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM Deposited 1998-08-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–224（224 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DAA 8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.206
1BS1 DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM 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 1–224（224 aa）	Not recorded	MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 DAA 8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUM FLUORIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.206
1BYI STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION Deposited 1998-10-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 0.97 Å
1DAD DETHIOBIOTIN SYNTHETASE COMPLEXED WITH ADP Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1DAE DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 3-(1-AMINOETHYL) NONANEDIOIC ACID Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	IKT 3-(1-AMINOETHYL)NONANEDIOIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1DAF DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID, ADP, AND CALCIUM Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	CA CALCIUM ION × 2 DSD 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1DAG DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	DSD 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.64 Å
1DAH DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7,8-DIAMINO-NONANOIC ACID, 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE, AND MANGANESE Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	MN MANGANESE (II) ION × 2 DNN 7,8-DIAMINO-NONANOIC ACID × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.64 Å
1DAI DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID Deposited 1995-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	DSD 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.64 Å
1DAK DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE Deposited 1998-03-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4 DPU MIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.60 Å R-free 0.210
1DAM DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM Deposited 1998-08-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	MG MAGNESIUM ION × 4 PO4 PHOSPHATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 DTB 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.80 Å R-free 0.233
1DBS MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE Deposited 1994-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1DTS CRYSTAL STRUCTURE OF AN ATP DEPENDENT CARBOXYLASE, DETHIOBIOTIN SYNTHASE, AT 1.65 ANGSTROMS RESOLUTION Deposited 1995-03-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å R-free 0.230

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIOD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 1–224

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	1a82
Deposition date deposition_date	1998-03-31
Structure title title	DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID
Keywords keywords	PHOSPHORYL TRANSFER, BIOTIN BIOSYNTHESIS, LIGASE; BIOTIN BIOSYNTHESIS
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	17.75 Å
Radius of gyration Rg (electron density) rg_electron	16.68 Å
Forward intensity I(0) i0	11160800.00
Molecular weight molecular_weight	24724.0 kDa
Excluded volume excluded_volume	30910 Å³
Envelope volume envelope_volume	34675 Å³
Hydration-shell volume shell_volume	17182 Å³
Envelope diameter envelope_diameter	57.5 Å
Shell Rg shell_rg	23.16 Å
Envelope Rg envelope_rg	17.09 Å
Shape Rg shape_rg	16.67 Å
Total Rg total_rg	17.72 Å
Total atoms total_atoms	1737
Residues n_residues	224
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	57.9 Å
Rg (real space) rg_real	17.64 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.1160e+07
I(0) uncertainty (real space) i0_real_error	1.4620e+05
Rg (reciprocal space) rg_reciprocal	17.65 Å
I(0) (reciprocal space) i0_reciprocal	11160000.0000
Solution quality estimate total_estimate	0.8051
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.319
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2539000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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	DETHIOBIOTIN SYNTHETASE
Molecular weight formula_weight	24028.3 kDa
EC 编号 ec_number	6.3.3.3
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	1956

SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL

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

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	7,8-DIAMINO-NONANOIC ACID
Molecular weight formula_weight	188.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 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	219

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a82a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	1a82A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	72.900 Å
Unit-cell length b length_b	47.900 Å
Unit-cell length c length_c	60.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2460

fit	/app/data/saxs_computation/a8/1a82/1a82.fit
pddf	/app/data/pr_computation/a8/1a82/1a82.pr.out
profile	/app/data/saxs_computation/a8/1a82/1a82.dat

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID

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

DETHIOBIOTIN SYNTHETASE

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