SAXSdb — 1adn

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

N-ADA 10

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 1–92	Not recorded	ZN ZINC ION × 1	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1ADN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EYF REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF E. COLI ADA Deposited 2000-05-06	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–92（92 aa） Fragment：N-TERMINAL 10 KDA DOMAIN	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Pressure ambient NMR measurement conditions pH 6.4；298 K；Pressure ambient NMR measurement conditions pH 6.4；298 K；Pressure ambient NMR measurement conditions pH 6.4；298 K；Pressure ambient NMR sample composition 2 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 100% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM N-Ada10 U-15N; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O \| 100% D2O NMR sample composition 2 mM N-Ada10 U-15N, 13C; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1SFE ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ESCHERICHIA COLI Deposited 1996-06-21	Different construct Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 175–354（180 aa） Fragment：C-TERMINAL 19KD OF THE ADA PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1U8B Crystal structure of the methylated N-ADA/DNA complex Deposited 2004-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 9–139（131 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；100 mM sodium cacodylate, 100 mM NaCl, 50 mM magnesium chloride, 20% OEG 8000, pH 6.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.274
1WPK Methylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein Deposited 2004-09-07	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–146（146 aa） Fragment：Methylated N-terminal 16 kDa Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 300mM NaCl；Pressure ambient NMR sample composition 1mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol NA; 85% H2O, 15% D2O \| 85% H2O, 15% D2O NMR sample composition 1mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol ; 99.9% D2O \| 99.9% D2O	Resolution not provided
1ZGW NMR structure of E. Coli Ada protein in complex with DNA Deposited 2005-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–139（139 aa） Fragment：N-terminal domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 25 mM sodium phosphate; 50 mM NaCl; 5 mM DTT；Pressure ambient NMR sample composition 13C; 15N; 70% 2H \| 90% H2O/10% D2O NMR sample composition 15N \| 90% H20, 10% D2O NMR sample composition 15N; Ile delta1, Leu delta1, delta2, Val gamma1, gamma2 13C; 2H \| D2O NMR sample composition Val, Ile, Leu Methyl group 13C; Phe and Tyr 1H; 2H \| 90% H2O/10% D2O NMR sample composition 15N, 2H \| 90% H2O/10% D2O NMR sample composition 10% 13C \| D2O NMR sample composition 13C C5A labeled thymine top or bottom strand; unlabeled protein \| D2O NMR sample composition 13C; 15N; 2H \| 90% H2O, 10% D20 NMR sample composition 13C \| D2O NMR sample composition 15N \| D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	ADA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–92； UniProt 1–92

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	1adn
Deposition date deposition_date	1993-09-30
Structure title title	SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA
Keywords keywords	TRANSCRIPTION REGULATION; TRANSCRIPTION REGULATION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.71 Å
Radius of gyration Rg (electron density) rg_electron	17.66 Å
Forward intensity I(0) i0	375534000.00
Molecular weight molecular_weight	147330.0 kDa
Excluded volume excluded_volume	179070 Å³
Envelope volume envelope_volume	71153 Å³
Hydration-shell volume shell_volume	24036 Å³
Envelope diameter envelope_diameter	93.4 Å
Shell Rg shell_rg	32.01 Å
Envelope Rg envelope_rg	26.86 Å
Shape Rg shape_rg	17.56 Å
Total Rg total_rg	18.55 Å
Total atoms total_atoms	10248
Residues n_residues	1288
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	48.3 Å
Rg (real space) rg_real	16.32 Å
Rg uncertainty (real space) rg_real_error	0.09 Å
I(0) (real space) i0_real	3.5700e+08
I(0) uncertainty (real space) i0_real_error	3.2010e+06
Rg (reciprocal space) rg_reciprocal	18.11 Å
I(0) (reciprocal space) i0_reciprocal	375500000.0000
Solution quality estimate total_estimate	0.6643
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	2.5350
Highest regularization parameter α highest_alpha	647700.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.005; Oscil: 0.905; Stabil: 0.991; Sysdev: 0.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1adna_
Class class	g — Small proteins
Fold Fold fold	g.48 — Ada DNA repair protein, N-terminal domain (N-Ada 10)
Superfamily Superfamily superfamily	g.48.1 — Ada DNA repair protein, N-terminal domain (N-Ada 10)
Family Family family	g.48.1.1 — Ada DNA repair protein, N-terminal domain (N-Ada 10)

CATH v4.4 (1 domains)

Domain ID domain_id	1adnA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	10 — DNA Methylphosphotriester Repair Domain
Homologous superfamily homologous superfamily	10 — DNA Methylphosphotriester Repair Domain

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	N-ADA 10
Molecular weight formula_weight	10470.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10248

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562

SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA

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

N-ADA 10

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/ad/1adn/1adn.fit
pddf	/app/data/pr_computation/ad/1adn/1adn.pr.out
profile	/app/data/saxs_computation/ad/1adn/1adn.dat