SAXSdb — 3uby

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

DNA-3-methyladenine glycosylase

Homo sapiens

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 84–298 Chain B； UniProt 84–298	Fragment：DELTA79AAG	;DNA (5'-D(GPAPCPAPTPGP(EDC)PTPTPGPCPCP*T)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. Crystals were obtained upon mixing 1 uL of protein-DNA complex and 1 uL of reservoir solution (100 mM BIS-TRIS, pH 5.5, 200 mM cesium chloride and 20% polyethylene glycol (PEG) 3350) over 0.5 ml of reservoir solution. Crystals appeared after incubation for 14 days at 22 degrees C, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.265

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 3UBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BNK HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA Deposited 1998-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 80–295（216 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.260
1EWN CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA Deposited 2000-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 80–298（219 aa） Fragment：E125Q	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；PEG 4000, MgCl2, Tris-HCl, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.259
1F4R CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA Deposited 2000-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 80–298（219 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, magnesium chloride, Tris-HCl, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.276
1F6O CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH DNA Deposited 2000-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 80–298（219 aa） Fragment：C-TERMINAL FRAGMENT	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.282
3QI5 Crystal structure of human alkyladenine DNA glycosylase in complex with 3,N4-ethenocystosine containing duplex DNA Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 84–298（215 aa） Fragment：delta79AAG	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary strand that contained G opposite EDC (5'-GGC AAG CAT GTC A-3'). The delta79AAG-EDC complexes were prepared by mixing equimolar ratios of delta79AAG and EDC:G 13-mer DNA duplex at the final protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM Hepes-NaOH pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. The crystals were obtained upon mixing 1 uL of complex and 1 ul of the reservoir solution (100 mM sodium cacodylate pH 6.0, 200 mM manganese chloride and 20% polyethylene glycol (PEG)-3350) over 0.5 ml of the reservoir solution, followed by incubation for 2 days, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.284
3QI5 Crystal structure of human alkyladenine DNA glycosylase in complex with 3,N4-ethenocystosine containing duplex DNA Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 84–298（215 aa） Fragment：delta79AAG	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary strand that contained G opposite EDC (5'-GGC AAG CAT GTC A-3'). The delta79AAG-EDC complexes were prepared by mixing equimolar ratios of delta79AAG and EDC:G 13-mer DNA duplex at the final protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM Hepes-NaOH pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. The crystals were obtained upon mixing 1 uL of complex and 1 ul of the reservoir solution (100 mM sodium cacodylate pH 6.0, 200 mM manganese chloride and 20% polyethylene glycol (PEG)-3350) over 0.5 ml of the reservoir solution, followed by incubation for 2 days, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.284
7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–298（298 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.90 Å
7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–298（298 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–298（298 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	3MG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–219； UniProt 84–298 Author chain B； PDBConstruct 5–219； UniProt 84–298

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	3uby
Deposition date deposition_date	2011-10-25
Structure title title	Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA
Keywords keywords	alkyladenine DNA glycosylase fold, AAG, DNA repair, DNA binding, Nucleus, HYDROLASE-DNA complex; HYDROLASE/DNA
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	27.47 Å
Radius of gyration Rg (electron density) rg_electron	26.34 Å
Forward intensity I(0) i0	43409500.00
Molecular weight molecular_weight	47569.0 kDa
Excluded volume excluded_volume	57995 Å³
Envelope volume envelope_volume	72446 Å³
Hydration-shell volume shell_volume	24046 Å³
Envelope diameter envelope_diameter	96.9 Å
Shell Rg shell_rg	32.10 Å
Envelope Rg envelope_rg	26.37 Å
Shape Rg shape_rg	26.29 Å
Total Rg total_rg	27.07 Å
Total atoms total_atoms	3321
Residues n_residues	399
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	94.2 Å
Rg (real space) rg_real	27.70 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	4.3410e+07
I(0) uncertainty (real space) i0_real_error	6.1080e+05
Rg (reciprocal space) rg_reciprocal	27.63 Å
I(0) (reciprocal space) i0_reciprocal	43410000.0000
Solution quality estimate total_estimate	0.8441
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.447
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5714000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.790; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA-3-methyladenine glycosylase
Molecular weight formula_weight	24314.9 kDa
EC 编号 ec_number	3.2.2.21
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3571

GPHMTRLGLEFFDQPAVPLARAFLGQVLVRRLPNGTELRGRIVETEAYLGPEDEAAHSRGGRQTPRNRGMFMKPGTLYVYIIYGMYFCMNISSQGDGACVLLRALEPLEGLETMRQLRSTLRKGTASRVLKDRELCSGPSKLCQALAINKSFDQRDLAQDEAVWLERGPLEPSEPAVVAAARVGVGHAGEWARKPLRFYVRGSPWVSVVDRVAEQDTQA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPCPAPTPGP(EDC)PTPTPGPCPCP*T)-3') ;
Molecular weight formula_weight	3966.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

GACATGXTTGCCT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ubya1
Class class	b — All beta proteins
Fold Fold fold	b.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
Family Family family	b.46.1.2 — 3-methyladenine DNA glycosylase (AAG, ANPG, MPG)

Domain ID domain_id	d3ubya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ubyb1
Class class	b — All beta proteins
Fold Fold fold	b.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamily	b.46.1 — FMT C-terminal domain-like
Family Family family	b.46.1.2 — 3-methyladenine DNA glycosylase (AAG, ANPG, MPG)

Domain ID domain_id	d3ubyb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3ubyA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	300 — 3-methyladenine DNA Glycosylase; Chain A
Homologous superfamily homologous superfamily	10 — Methylpurine-DNA glycosylase (MPG)

Domain ID domain_id	3ubyB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	300 — 3-methyladenine DNA Glycosylase; Chain A
Homologous superfamily homologous superfamily	10 — Methylpurine-DNA glycosylase (MPG)

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8. Citations (1)

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Unit-cell length a length_a	41.168 Å
Unit-cell length b length_b	41.168 Å
Unit-cell length c length_c	262.546 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	65.650 Å
R factor r_factor	0.2218
R_work r_work	0.2194
R_free r_free	0.2655

fit	/app/data/saxs_computation/ub/3uby/3uby.fit
pddf	/app/data/pr_computation/ub/3uby/3uby.pr.out
profile	/app/data/saxs_computation/ub/3uby/3uby.dat

Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA

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

DNA-3-methyladenine glycosylase

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)