SAXSdb — 6asc

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

Nuclease SbcCD subunit D

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 (5E)-3-butyl-5-[(4-hydroxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one × 2 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1X0_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–336； UniProt 2–324 Author chain B； PDBConstruct 14–336； UniProt 2–324

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	6asc
Deposition date deposition_date	2017-08-24
Structure title title	Mre11 dimer in complex with Endonuclease inhibitor PFM04
Keywords keywords	DNA REPAIR MRE11 THERMOPHILIC NUCLEASE DNA DOUBLE-STRAND BREAK REPAIR HYDROLASE, hydrolase-hydrolase inhibitor complex; hydrolase/hydrolase inhibitor
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.

6asc__assembly_1__model_1

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

Download this curve (.dat)

6asc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6asc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.22 Å
Rg (electron density)	30.70 Å
Total Rg	31.22 Å
Atom count	5230
Residues	652
Excluded volume	93711 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6asc__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Nuclease SbcCD subunit D
Molecular weight formula_weight	38575.2 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	5375

MGSDKIHHHHHHVINLKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIE

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(5E)-3-butyl-5-[(4-hydroxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one
Molecular weight formula_weight	293.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6ascA01
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	6ascA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	210 — DNA double-strand break repair nuclease

Domain ID domain_id	6ascB01
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	6ascB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	210 — DNA double-strand break repair nuclease

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Unit-cell length a length_a	48.053 Å
Unit-cell length b length_b	112.682 Å
Unit-cell length c length_c	81.162 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.26 °
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	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	46.038 Å
R factor r_factor	0.1984
R_work r_work	0.1969
R_free r_free	0.2318

Mre11 dimer in complex with Endonuclease inhibitor PFM04

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

Nuclease SbcCD subunit D

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

6asc__assembly_1__model_1

6asc__assembly_1__model_1 | I(q)

6asc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Mre11 dimer in complex with Endonuclease inhibitor PFM04

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

Nuclease SbcCD subunit D

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

6asc__assembly_1__model_1

6asc__assembly_1__model_1 | I(q)

6asc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)