SAXSdb — 4w9m

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

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

Thermotoga maritima MSB8

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 (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCPC)-3') ; × 1 ;DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCPC)-3') ; × 1 Exonuclease, putative × 2 （Q9X1X0） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	;DNA (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCPC)-3') ; × 1 ;DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCPC)-3') ; × 1 Exonuclease, putative × 2 （Q9X1X0） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD50_THEMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–188； UniProt 1–188 Author chain C； PDBConstruct 200–365； UniProt 687–852 Author chain E； PDBConstruct 1–188； UniProt 1–188 Author chain E； PDBConstruct 200–365； UniProt 687–852 Author chain I； PDBConstruct 1–188； UniProt 1–188 Author chain I； PDBConstruct 200–365； UniProt 687–852 Author chain K； PDBConstruct 1–188； UniProt 1–188 Author chain K； PDBConstruct 200–365； UniProt 687–852

Exonuclease, putative

Thermotoga maritima MSB8

UniProt Q9X1X0

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 (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCPC)-3') ; × 1 ;DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCPC)-3') ; × 1 Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase × 2 （Q9X1X1） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	;DNA (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCPC)-3') ; × 1 ;DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCPC)-3') ; × 1 Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase × 2 （Q9X1X1） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1X0_THEMA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–37； UniProt 347–383 Author chain F； PDBConstruct 1–37； UniProt 347–383 Author chain J； PDBConstruct 1–37； UniProt 347–383 Author chain L； PDBConstruct 1–37； UniProt 347–383

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	4w9m
Deposition date deposition_date	2014-08-27
Structure title title	AMPPNP bound Rad50 in complex with dsDNA
Keywords keywords	ATPase, DNA AMPPNP bound, hydrolase; HYDROLASE
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.

4w9m__assembly_1__model_1

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

Download this curve (.dat)

4w9m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4w9m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.32 Å
Rg (electron density)	32.99 Å
Total Rg	33.80 Å
Atom count	6952
Residues	805
Excluded volume	122500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4w9m__assembly_1__model_1`	Hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4w9m__assembly_2__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 (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCP*C)-3') ;
Molecular weight formula_weight	4611.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y,Z
Atom count atom_count	14169

GGTCGGTGACCGACC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCP*C)-3') ;
Molecular weight formula_weight	4571.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,G

GGTCGGTCACCGACC

Entity 3 Entity 3 polymer

Description description	Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
Molecular weight formula_weight	41073.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E,I,K

MRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYPNSYDYVNRNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITEIISDVFQSKETLEKLEKLLKEKMKKLENEISSGGAGGAGGSLEKKLKEMSDEYNNLDLLRKYLFDKSNFSRYFTGRVLEAVLKRTKAYLDILTNGRFDIDFDDEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLDTENKEKIASVLKELERLNKVIVFITHDREFSEAFDRKLRITGGVVVNE

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Exonuclease, putative
Molecular weight formula_weight	4650.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,J,L

DKLDYFELFKEYLKKREENHEKLLKILDELLDEVKKS

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	4w9mC01
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	4w9mE01
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	4w9mI01
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	4w9mK01
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	4w9mK02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	660 — Helix hairpin bin

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Unit-cell length a length_a	49.713 Å
Unit-cell length b length_b	96.386 Å
Unit-cell length c length_c	105.926 Å
Unit-cell angle α angle_alpha	90.01 °
Unit-cell angle β angle_beta	89.22 °
Unit-cell angle γ angle_gamma	81.67 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.685 Å
R factor r_factor	0.2176
R_work r_work	0.2148
R_free r_free	0.2704

AMPPNP bound Rad50 in complex with dsDNA

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

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

State in the Current Structure

Other States of the Same Protein in the Database

Exonuclease, putative

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

4w9m__assembly_1__model_1

4w9m__assembly_1__model_1 | I(q)

4w9m__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

AMPPNP bound Rad50 in complex with dsDNA

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

Probable DNA double-strand break repair Rad50 ATPase,Probable 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

Exonuclease, putative

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

4w9m__assembly_1__model_1

4w9m__assembly_1__model_1 | I(q)

4w9m__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)