SAXSdb — 6nua

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

SOS response-associated peptidase YedK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(GPTPCP(PED)PGPGP*A)-3') ; × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(GPTPCP(PED)PGPGP*A)-3') ; × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YEDK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 2–222 Author chain B； PDBConstruct 1–221； UniProt 2–222

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	6nua
Deposition date deposition_date	2019-01-31
Structure title title	DNA-protein crosslink between E. coli YedK and ssDNA containing an abasic site
Keywords keywords	DNA-protein crosslink, abasic site, thiazolidine, replication stress, DNA BINDING PROTEIN, dna binding protein-dna complex; dna binding protein/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.

6nua__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6nua__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nua__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.39 Å
Rg (electron density)	17.22 Å
Total Rg	18.17 Å
Atom count	3762
Residues	233
Excluded volume	33934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nua__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nua__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	SOS response-associated peptidase YedK
Molecular weight formula_weight	25606.9 kDa
EC 编号 ec_number	3.4.-.-
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	7810

CGRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPVLEVLFQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPTPCP(PED)PGPGP*A)-3') ;
Molecular weight formula_weight	2031.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

GTCXGGA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6nuaA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1680 — hypothetical protein yedk fold
Homologous superfamily homologous superfamily	10 — SOS response associated peptidase-like

Domain ID domain_id	6nuaB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1680 — hypothetical protein yedk fold
Homologous superfamily homologous superfamily	10 — SOS response associated peptidase-like

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Unit-cell length a length_a	61.258 Å
Unit-cell length b length_b	41.886 Å
Unit-cell length c length_c	81.423 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.78 °
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	1.640 Å
Low-resolution limit resolution_low	40.504 Å
R factor r_factor	0.1733
R_work r_work	0.1708
R_free r_free	0.2216

DNA-protein crosslink between E. coli YedK and ssDNA containing an abasic site

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

SOS response-associated peptidase YedK

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

6nua__assembly_2__model_1

6nua__assembly_2__model_1 | I(q)

6nua__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

DNA-protein crosslink between E. coli YedK and ssDNA containing an abasic site

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

SOS response-associated peptidase YedK

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

6nua__assembly_2__model_1

6nua__assembly_2__model_1 | I(q)

6nua__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)