SAXSdb — 4ew4

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

Methyl-CpG-binding domain protein 4

Mus musculus

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	;DNA (5'-D(TPCPAPGPCPGPCPAPTPGPG)-3') ; × 1 ;DNA (5'-D(CPCPAPTPGP(3DR)PGPCPTPGPA)-3') ; × 1 NICKEL (II) ION × 1 UNKNOWN ATOM OR ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MBD4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–146； UniProt 411–554

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	4ew4
Deposition date deposition_date	2012-04-26
Structure title title	mouse MBD4 glycosylase domain in complex with DNA containing a ribose sugar
Keywords keywords	stable intermediate, N-glycosidic bond, Helix-hairpin-Helix, DNA glycosylase, HYDROLASE-DNA complex; HYDROLASE/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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ew4__assembly_1__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	Methyl-CpG-binding domain protein 4
Molecular weight formula_weight	17564.2 kDa
EC 编号 ec_number	3.2.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1636

HMKWTPPRSPFNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPAPGPCPGPCPAPTPGP*G)-3') ;
Molecular weight formula_weight	3374.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

TCAGCGCATGG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPCPAPTPGP(3DR)PGPCPTPGP*A)-3') ;
Molecular weight formula_weight	3225.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CCATGNGCTGA

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	UNKNOWN ATOM OR ION
Molecular weight formula_weight	103.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4ew4A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

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Unit-cell length a length_a	40.120 Å
Unit-cell length b length_b	110.300 Å
Unit-cell length c length_c	119.710 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.791 Å
Low-resolution limit resolution_low	27.400 Å
R factor r_factor	0.2604
R_work r_work	0.2594
R_free r_free	0.2766

mouse MBD4 glycosylase domain in complex with DNA containing a ribose sugar

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

Methyl-CpG-binding domain protein 4

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

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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

mouse MBD4 glycosylase domain in complex with DNA containing a ribose sugar

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

Methyl-CpG-binding domain protein 4

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

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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)