SAXSdb — 1dah

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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	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 experimental conditions	Resolution 1.64 Å

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 1DAH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A82 DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID 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	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
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 experimental conditions 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 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 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 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	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
1DAI DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID Deposited 1995-05-08	Different ligand/ion	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 experimental conditions 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 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 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	1dah
Deposition date deposition_date	1995-05-08
Structure title title	DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7,8-DIAMINO-NONANOIC ACID, 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE, AND MANGANESE
Keywords keywords	LIGASE, BIOTIN BIOSYNTHESIS, MAGNESIUM, ATP-BINDING; LIGASE
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	17.90 Å
Radius of gyration Rg (electron density) rg_electron	16.83 Å
Forward intensity I(0) i0	11138600.00
Molecular weight molecular_weight	24753.0 kDa
Excluded volume excluded_volume	30941 Å³
Envelope volume envelope_volume	34967 Å³
Hydration-shell volume shell_volume	17244 Å³
Envelope diameter envelope_diameter	58.1 Å
Shell Rg shell_rg	23.28 Å
Envelope Rg envelope_rg	17.19 Å
Shape Rg shape_rg	16.84 Å
Total Rg total_rg	17.82 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	56.9 Å
Rg (real space) rg_real	17.79 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.1140e+07
I(0) uncertainty (real space) i0_real_error	1.4420e+05
Rg (reciprocal space) rg_reciprocal	17.80 Å
I(0) (reciprocal space) i0_reciprocal	11140000.0000
Solution quality estimate total_estimate	0.8071
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2463000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; 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	1879

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	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 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	142

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1daha_
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	1dahA00
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 (2)

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Unit-cell length a length_a	73.200 Å
Unit-cell length b length_b	49.200 Å
Unit-cell length c length_c	61.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.10 °
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	1.640 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	—

fit	/app/data/saxs_computation/da/1dah/1dah.fit
pddf	/app/data/pr_computation/da/1dah/1dah.pr.out
profile	/app/data/saxs_computation/da/1dah/1dah.dat

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7,8-DIAMINO-NONANOIC ACID, 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE, AND MANGANESE