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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 2 DNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 138–331 Chain M； UniProt 138–331	Not recorded	;DNA (5'-D(PAPCPG)-3') ; × 1 SO4* SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；297 K；Ammonium sulphate	Resolution 2.48 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7U02	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TZV Structure of DriD C-domain bound to 9mer ssDNA Deposited 2022-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 138–331（194 aa） Chain M 138–331（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；0.1 M MES pH 6.5, 0.1 M Imidazole, 20% PEG 8000	Resolution 1.65 Å R-free 0.223
9CU3 Allosteric mechanism of DriD transcription activator Deposited 2024-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 82–331（250 aa） Chain B 82–331（250 aa）	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298.15 K；Ammonium sulfate dibasic, sodium cacodylate trihydrate	Resolution 1.90 Å R-free 0.231
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric	Chain Q 1–331（331 aa） Chain R 1–331（331 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric	Chain Q 1–331（331 aa） Chain R 1–331（331 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9PGA The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex Deposited 2025-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric	Chain Q 1–331（331 aa） Chain R 1–331（331 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.95 Å
Radius of gyration Rg (electron density) rg_electron	22.00 Å
Forward intensity I(0) i0	33033000.00
Molecular weight molecular_weight	42973.0 kDa
Excluded volume excluded_volume	53302 Å³
Envelope volume envelope_volume	65800 Å³
Hydration-shell volume shell_volume	25011 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	28.71 Å
Envelope Rg envelope_rg	21.96 Å
Shape Rg shape_rg	21.96 Å
Total Rg total_rg	22.94 Å
Total atoms total_atoms	3031
Residues n_residues	388
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	68.3 Å
Rg (real space) rg_real	22.80 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.3030e+07
I(0) uncertainty (real space) i0_real_error	4.0190e+05
Rg (reciprocal space) rg_reciprocal	22.84 Å
I(0) (reciprocal space) i0_reciprocal	33030000.0000
Solution quality estimate total_estimate	0.9150
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.2 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.589
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6326000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Caulobacter vibrioides (strain ATCC 19089 / CB15)
通用名 common_name	Caulobacter crescentus
NCBI Class编号 ncbi_taxonomy_id	190650
宿主生物 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/u0/7u02/7u02.fit
pddf	/app/data/pr_computation/u0/7u02/7u02.pr.out
profile	/app/data/saxs_computation/u0/7u02/7u02.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)