SAXSdb — 5dny

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

DNA double-strand break repair protein Mre11

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase × 2 （Q58718） DNA (27-MER) × 1 DNA (27-MER) × 1 MAGNESIUM ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MRE11_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–386； UniProt 1–366 Author chain C； PDBConstruct 21–386； UniProt 1–366

DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt Q58718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA double-strand break repair protein Mre11 × 2 （Q58719） DNA (27-MER) × 1 DNA (27-MER) × 1 MAGNESIUM ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD50_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–190； UniProt 1–190 Author chain B； PDBConstruct 191–371； UniProt 825–1005 Author chain D； PDBConstruct 1–190； UniProt 1–190 Author chain D； PDBConstruct 191–371； UniProt 825–1005

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	5dny
Deposition date deposition_date	2015-09-10
Structure title title	Structure of the ATPrS-Mre11/Rad50-DNA complex
Keywords keywords	Nuclease, RECOMBINATION-DNA complex; RECOMBINATION/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.

5dny__assembly_1__model_1

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

Download this curve (.dat)

5dny__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dny__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.77 Å
Rg (electron density)	38.22 Å
Total Rg	38.58 Å
Atom count	12656
Residues	1468
Excluded volume	224060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dny__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	DNA double-strand break repair protein Mre11
Molecular weight formula_weight	45370.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12658

MGSSHHHHHHSSGLVPRGSHMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPDNVDIESLNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFRG

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase
Molecular weight formula_weight	42389.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA (27-MER)
Molecular weight formula_weight	8364.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AAAGTTGGGATTGAGACACACATTCGT

Entity 4 Entity 4 polymer

Description description	DNA (27-MER)
Molecular weight formula_weight	8226.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TTACGAATGTGTGTCTCAATCCCAACT

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5dnyA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	5dnyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	5dnyA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	10 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 — Mre11, C-terminal domain-like

Domain ID domain_id	5dnyB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dnyC01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	5dnyC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	5dnyC03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	10 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 — Mre11, C-terminal domain-like

Domain ID domain_id	5dnyD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	84.303 Å
Unit-cell length b length_b	130.111 Å
Unit-cell length c length_c	166.656 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	3.110 Å
Low-resolution limit resolution_low	40.865 Å
R factor r_factor	0.2239
R_work r_work	0.2211
R_free r_free	0.2733

Structure of the ATPrS-Mre11/Rad50-DNA complex

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

DNA double-strand break repair protein Mre11

State in the Current Structure

Other States of the Same Protein in the Database

DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase

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

5dny__assembly_1__model_1

5dny__assembly_1__model_1 | I(q)

5dny__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the ATPrS-Mre11/Rad50-DNA complex

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

DNA double-strand break repair protein Mre11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase

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

5dny__assembly_1__model_1

5dny__assembly_1__model_1 | I(q)

5dny__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)