SAXSdb — 7p0l

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

DNA damage response protein Mdb1

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Histone H2A-beta × 1 （P04910） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H2A-beta × 1 （P04910） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDB1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–199； UniProt 384–581 Author chain B； PDBConstruct 2–199； UniProt 384–581

Histone H2A-beta

OrganismNot specified

UniProt P04910

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA damage response protein Mdb1 × 1 （O14079） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA damage response protein Mdb1 × 1 （O14079） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A2_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–11； UniProt 125–131 Author chain D； PDBConstruct 5–11； UniProt 125–131

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	7p0l
Deposition date deposition_date	2021-06-29
Structure title title	Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide
Keywords keywords	DNA damage response, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

7p0l__assembly_1__model_1

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

Download this curve (.dat)

7p0l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7p0l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.85 Å
Rg (electron density)	19.00 Å
Total Rg	19.87 Å
Atom count	3223
Residues	200
Excluded volume	28647 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7p0l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7p0l__assembly_2__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	DNA damage response protein Mdb1
Molecular weight formula_weight	22696.9 kDa
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	6364

MNKHTNLVTSSFNLTKPMKSFIRRNGLRVQESVTDETDFVILGSPPLRRTHKFLLATSLGIPLVSSQYLTDCIKSGKVLDFRSYKYKDEEAEAKWGFRLDDIHRRTCFNGKRLYITKAIRDSMVGDSIHGLYSILETSGAEIVGDIKRAQEKDTIILAQPDNDQEGRNMSATGLNVYKIELVALSILRDRIDFDEFLID

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2A-beta
Molecular weight formula_weight	1241.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SGRTGKPSQEL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7p0lA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	7p0lA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	7p0lB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	7p0lB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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Unit-cell length a length_a	41.380 Å
Unit-cell length b length_b	42.050 Å
Unit-cell length c length_c	96.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	48.120 Å
R factor r_factor	0.2098
R_work r_work	0.2078
R_free r_free	0.2467

Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide

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

DNA damage response protein Mdb1

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A-beta

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

7p0l__assembly_1__model_1

7p0l__assembly_1__model_1 | I(q)

7p0l__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide

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

DNA damage response protein Mdb1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A-beta

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

7p0l__assembly_1__model_1

7p0l__assembly_1__model_1 | I(q)

7p0l__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)