SAXSdb — 3ubt

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

Modification methylase HaeIII

Haemophilus aegyptius

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 Y； UniProt 1–330	Mutation：C71S	5'-D(TPGPGPCPCPA)-3' × 2 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
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–330	Mutation：C71S	5'-D(TPGPGPCPCPA)-3' × 2 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
3	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–330	Mutation：C71S	5'-D(TPGPGPCPCPA)-3' × 2 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

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 3UBT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DCT DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA Deposited 1995-05-17	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 A 1–324（324 aa）	Not recorded	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
1DCT DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA Deposited 1995-05-17	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 B 1–324（324 aa）	Not recorded	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

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTH3_HAEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 1–330 Author chain B； PDBConstruct 1–330； UniProt 1–330 Author chain Y； PDBConstruct 1–330； UniProt 1–330

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	3ubt
Deposition date deposition_date	2011-10-24
Structure title title	Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA
Keywords keywords	;Protein-DNA complex, DNA cytosine-5 methyltransferase, DNA binding, S-Adenosyl methionine binding, Cytosine-5 DNA methylation, 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	32.61 Å
Radius of gyration Rg (electron density) rg_electron	32.65 Å
Forward intensity I(0) i0	259971000.00
Molecular weight molecular_weight	123570.0 kDa
Excluded volume excluded_volume	152120 Å³
Envelope volume envelope_volume	195600 Å³
Hydration-shell volume shell_volume	49164 Å³
Envelope diameter envelope_diameter	108.1 Å
Shell Rg shell_rg	40.17 Å
Envelope Rg envelope_rg	32.11 Å
Shape Rg shape_rg	32.67 Å
Total Rg total_rg	33.14 Å
Total atoms total_atoms	8668
Residues n_residues	1020
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	101.9 Å
Rg (real space) rg_real	32.43 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.6000e+08
I(0) uncertainty (real space) i0_real_error	3.7560e+06
Rg (reciprocal space) rg_reciprocal	32.51 Å
I(0) (reciprocal space) i0_reciprocal	260000000.0000
Solution quality estimate total_estimate	0.9033
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.6 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74500000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Modification methylase HaeIII
Molecular weight formula_weight	37837.3 kDa
EC 编号 ec_number	2.1.1.37
Mutation mutation	C71S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,A,B
Atom count atom_count	9258

MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPSQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICKGNN

来源 Source

来源生物 organism	Haemophilus aegyptius
通用名 common_name	Koch-Weeks bacillus
NCBI Class编号 ncbi_taxonomy_id	197575
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(TPGPGPCPCPA)-3'
Molecular weight formula_weight	1809.2 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E,F,G,H,C

TGGCCA

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

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	3

Entity 5 Entity 5 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	568

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ubta_
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	d3ubtb_
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	d3ubty_
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 (6 domains)

Domain ID domain_id	3ubtA01
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	3ubtA02
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	3ubtB01
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	3ubtB02
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	3ubtY01
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	3ubtY02
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 (1)

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Unit-cell length a length_a	57.564 Å
Unit-cell length b length_b	129.588 Å
Unit-cell length c length_c	132.381 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.502 Å
Low-resolution limit resolution_low	16.981 Å
R factor r_factor	0.1841
R_work r_work	0.1822
R_free r_free	0.2212

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

Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA

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

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)