1yfj

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

Method: X-RAY DIFFRACTION

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

DNA adenine methylase

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3' × 2 CHLORIDE ION × 3 CALCIUM ION × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3' × 2 CHLORIDE ION × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3' × 2 CALCIUM ION × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 3	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3' × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 3	Consistent with all polymers
5	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3' × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers
6	Protein monomer	Monomer	Protein 1	S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DMA_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 1–259 Author chain B； PDBConstruct 1–259； UniProt 1–259 Author chain C； PDBConstruct 1–259； UniProt 1–259 Author chain D； PDBConstruct 1–259； UniProt 1–259 Author chain E； PDBConstruct 1–259； UniProt 1–259 Author chain F； PDBConstruct 1–259； UniProt 1–259

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	1yfj
Deposition date deposition_date	2005-01-02
Structure title title	T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact
Keywords keywords	T4DAM, METHYLTRANSFERASE, DNA, PROTEIN-DNA COMPLEX, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1yfj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yfj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yfj__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.15 Å
Rg (electron density)	22.91 Å
Total Rg	23.71 Å
Atom count	2747
Residues	289
Excluded volume	47062 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yfj__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yfj__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yfj__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yfj__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1yfj__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1yfj__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	5'-D(TPCPAPCPAPGPGPAPTPCPCPTPGPTP*G)-3'
Molecular weight formula_weight	4585.0 kDa
Source method src_method	syn
Copy count entity_count	10

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	1,2,3,4,5,6,7,8,9,0
Atom count atom_count	15008

TCACAGGATCCTGTG

Entity 2 Entity 2 polymer

Description description	DNA adenine methylase
Molecular weight formula_weight	30461.9 kDa
EC 编号 ec_number	2.1.1.72
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F

MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

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	4

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

Entity 5 Entity 5 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yfja1
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

Domain ID domain_id	d1yfjb_
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

Domain ID domain_id	d1yfjc_
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

Domain ID domain_id	d1yfjd_
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

Domain ID domain_id	d1yfje_
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

Domain ID domain_id	d1yfjf_
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.66.1.28 — N6 adenine-specific DNA methylase, DAM

CATH v4.4 (12 domains)

Domain ID domain_id	1yfjA01
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	1yfjA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

Domain ID domain_id	1yfjB01
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	1yfjB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

Domain ID domain_id	1yfjC01
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	1yfjC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

Domain ID domain_id	1yfjD01
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	1yfjD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

Domain ID domain_id	1yfjE01
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	1yfjE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

Domain ID domain_id	1yfjF01
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	1yfjF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1020 — Adenine-specific Methyltransferase; domain 2
Homologous superfamily homologous superfamily	10 — Adenine-specific Methyltransferase, Domain 2

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Unit-cell length a length_a	111.200 Å
Unit-cell length b length_b	133.000 Å
Unit-cell length c length_c	189.200 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	40

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

Resolution resolution	2.690 Å
Low-resolution limit resolution_low	34.780 Å
R factor r_factor	0.2060
R_work r_work	0.2020
R_free r_free	0.2500

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

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

DNA adenine methylase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yfj__assembly_2__model_1

1yfj__assembly_2__model_1 | I(q)

1yfj__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

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

DNA adenine methylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yfj__assembly_2__model_1

1yfj__assembly_2__model_1 | I(q)

1yfj__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)