SAXSdb — 1dct

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

PROTEIN (MODIFICATION METHYLASE HAEIII)

OrganismNot specified

UniProt P20589

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–324	Not recorded	;DNA (5'-D(APCPCPAPGPCPAPGPGP(C49)PCPAPCPCPAPGPTPG)-3') ; × 1 ;DNA (5'-D(TPCPAPCPTPGPGPTPGPGP(C5M)PCPTPGPCPTPGPG)-3') ; × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K	Resolution 2.80 Å R-free 0.326
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–324	Not recorded	;DNA (5'-D(APCPCPAPGPCPAPGPGP(C49)PCPAPCPCPAPGPTPG)-3') ; × 1 ;DNA (5'-D(TPCPAPCPTPGPGPTPGPGP(C5M)PCPTPGPCPTPGPG)-3') ; × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K	Resolution 2.80 Å R-free 0.326

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 1DCT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UBT Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA Deposited 2011-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain Y 1–330（330 aa）	Mutation：C71S	CL CHLORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；26-27% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100 mM ammonium sulfate, 50 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.221
3UBT Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA Deposited 2011-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–330（330 aa）	Mutation：C71S	CL CHLORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；26-27% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100 mM ammonium sulfate, 50 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.221
3UBT Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA Deposited 2011-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–330（330 aa）	Mutation：C71S	CL CHLORIDE ION × 1 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；26-27% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100 mM ammonium sulfate, 50 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	MTH3_HAEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–324； UniProt 1–324 Author chain B； PDBConstruct 1–324； UniProt 1–324

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	1dct
Deposition date deposition_date	1995-05-17
Structure title title	DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA
Keywords keywords	ENZYME, CYTOSINE METHYLASE, TRANSFERASE-DNA COMPLEX; TRANSFERASE/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	31.12 Å
Radius of gyration Rg (electron density) rg_electron	31.04 Å
Forward intensity I(0) i0	181716000.00
Molecular weight molecular_weight	95408.0 kDa
Excluded volume excluded_volume	114040 Å³
Envelope volume envelope_volume	143060 Å³
Hydration-shell volume shell_volume	38732 Å³
Envelope diameter envelope_diameter	105.7 Å
Shell Rg shell_rg	37.79 Å
Envelope Rg envelope_rg	30.76 Å
Shape Rg shape_rg	31.03 Å
Total Rg total_rg	31.55 Å
Total atoms total_atoms	6908
Residues n_residues	713
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	100.4 Å
Rg (real space) rg_real	31.15 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.8170e+08
I(0) uncertainty (real space) i0_real_error	2.7580e+06
Rg (reciprocal space) rg_reciprocal	31.14 Å
I(0) (reciprocal space) i0_reciprocal	181700000.0000
Solution quality estimate total_estimate	0.8933
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.504
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24390000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.931

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPCPAPGPCPAPGPGP(C49)PCPAPCPCPAPGPTPG)-3') ;
Molecular weight formula_weight	5559.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,G
Atom count atom_count	6908

ACCAGCAGGCCACCAGTG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPAPCPTPGPGPTPGPGP(C5M)PCPTPGPCPTPGPG)-3') ;
Molecular weight formula_weight	5553.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,N

TCACTGGTGGCCTGCTGG

Entity 3 Entity 3 polymer

Description description	PROTEIN (MODIFICATION METHYLASE HAEIII)
Molecular weight formula_weight	37093.6 kDa
EC 编号 ec_number	2.1.1.73
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSAL

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dcta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.26 — C5 cytosine-specific DNA methylase, DCM

Domain ID domain_id	d1dctb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.26 — C5 cytosine-specific DNA methylase, DCM

CATH v4.4 (4 domains)

Domain ID domain_id	1dctA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dctA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Methylase, subunit A, domain 2

Domain ID domain_id	1dctB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dctB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Methylase, subunit A, domain 2

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8. Citations (2)

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Unit-cell length a length_a	57.570 Å
Unit-cell length b length_b	108.040 Å
Unit-cell length c length_c	155.790 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.3260

fit	/app/data/saxs_computation/dc/1dct/1dct.fit
pddf	/app/data/pr_computation/dc/1dct/1dct.pr.out
profile	/app/data/saxs_computation/dc/1dct/1dct.dat

DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA

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

PROTEIN (MODIFICATION METHYLASE HAEIII)

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)