SAXSdb — 7u02

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

WYL domain-containing protein

Caulobacter vibrioides (strain ATCC 19089 / CB15)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 1	;DNA (5'-D(PAPCP*G)-3') ; × 1 SULFATE ION × 3 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9A999_CAUVC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–195； UniProt 138–331 Author chain M； PDBConstruct 2–195； UniProt 138–331

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	7u02
Deposition date deposition_date	2022-02-17
Structure title title	Structure of the C. crescentus DriD C-domain bound to ssDNA
Keywords keywords	DriD, DNA repair, SOS-independent repair, DidA, TRANSCRIPTION; TRANSCRIPTION
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.

7u02__assembly_1__model_1

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

Download this curve (.dat)

7u02__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7u02__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.95 Å
Rg (electron density)	22.00 Å
Total Rg	22.94 Å
Atom count	3031
Residues	388
Excluded volume	53302 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7u02__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	WYL domain-containing protein
Molecular weight formula_weight	21750.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,M
Atom count atom_count	3033

METIAVHAGPRPYEDQAVLGAIRAAIKGLQALSFRYEGGSTPGRTREVTPLGVLFGRSNYLVALEGKGGKPRSWRLDRMSDLKVLDKPAPPPQDFSLQAFADESFGIYHDEIQDVVLRIHKSRAEDALRWRFHATQQVTPEADGSVLVTFRAGGMRELSWHLFTWGDAVEIVAPQVLKDMMVQELREAGRAHGAW

Source Source

Source organism organism	Caulobacter vibrioides (strain ATCC 19089 / CB15)
Common name common_name	Caulobacter crescentus
NCBI taxonomy ID ncbi_taxonomy_id	190650
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPCP*G)-3') ;
Molecular weight formula_weight	886.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

ACG

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 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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Unit-cell length a length_a	87.400 Å
Unit-cell length b length_b	87.400 Å
Unit-cell length c length_c	139.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	66.540 Å
R factor r_factor	0.2338
R_work r_work	0.2303
R_free r_free	0.2790

Structure of the C. crescentus DriD C-domain bound to ssDNA

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

WYL domain-containing protein

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

7u02__assembly_1__model_1

7u02__assembly_1__model_1 | I(q)

7u02__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Structure of the C. crescentus DriD C-domain bound to ssDNA

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

WYL domain-containing protein

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

7u02__assembly_1__model_1

7u02__assembly_1__model_1 | I(q)

7u02__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)