SAXSdb — 2dwm

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

Primosomal protein N

Escherichia coli

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 A； UniProt 1–105 Chain B； UniProt 1–105	Fragment：Residues 1-105	5'-D(APT)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.318
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 1–105 Chain D； UniProt 1–105	Fragment：Residues 1-105	5'-D(APT)-3' × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.318

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 2DWM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–105（105 aa） Fragment：DNA binding domein Chain B 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–105（105 aa） Fragment：DNA binding domein Chain D 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–105（105 aa） Fragment：DNA binding domein Chain B 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–105（105 aa） Fragment：DNA binding domein Chain D 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7G Crystal structure of the aa complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–105（105 aa） Fragment：residues 1-105 Chain B 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；12% PEG 6000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
2D7G Crystal structure of the aa complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–105（105 aa） Fragment：residues 1-105 Chain D 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；12% PEG 6000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
2D7H Crystal structure of the ccc complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: pentameric	Chain A 1–105（105 aa） Fragment：residues 1-105 Chain B 1–105（105 aa） Fragment：residues 1-105 Chain C 1–105（105 aa） Fragment：residues 1-105 Chain D 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.293
2DWL Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.302
2DWL Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.302
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
6DCR E. coli PriA helicase winged helix domain deletion protein Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–732（732 aa）	Mutation：delta 114-174	ZN ZINC ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride	Resolution 1.98 Å R-free 0.215
6DCR E. coli PriA helicase winged helix domain deletion protein Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–732（732 aa）	Mutation：delta 114-174	ZN ZINC ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride	Resolution 1.98 Å R-free 0.215
8FAK DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli Deposited 2022-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain H 1–732（732 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9ZBT Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric	Chain H 1–732（732 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9ZBU Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric	Chain H 2–732（731 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

9 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 1–105 Author chain B； PDBConstruct 1–105； UniProt 1–105 Author chain C； PDBConstruct 1–105； UniProt 1–105 Author chain D； PDBConstruct 1–105； UniProt 1–105

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	2dwm
Deposition date deposition_date	2006-08-15
Structure title title	Crystal structure of the PriA protein complexed with oligonucleotides
Keywords keywords	PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	27.14 Å
Radius of gyration Rg (electron density) rg_electron	26.71 Å
Forward intensity I(0) i0	33657200.00
Molecular weight molecular_weight	47730.0 kDa
Excluded volume excluded_volume	61014 Å³
Envelope volume envelope_volume	78382 Å³
Hydration-shell volume shell_volume	25468 Å³
Envelope diameter envelope_diameter	90.1 Å
Shell Rg shell_rg	32.89 Å
Envelope Rg envelope_rg	26.67 Å
Shape Rg shape_rg	26.71 Å
Total Rg total_rg	27.45 Å
Total atoms total_atoms	3374
Residues n_residues	420
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	88.1 Å
Rg (real space) rg_real	27.22 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.3660e+07
I(0) uncertainty (real space) i0_real_error	4.2230e+05
Rg (reciprocal space) rg_reciprocal	27.20 Å
I(0) (reciprocal space) i0_reciprocal	33660000.0000
Solution quality estimate total_estimate	0.7241
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.385
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7635000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.960; Smooth: 0.910

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2dwmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily	60 — PriA, 3(prime) DNA-binding domain

Domain ID domain_id	2dwmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily	60 — PriA, 3(prime) DNA-binding domain

Domain ID domain_id	2dwmC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily	60 — PriA, 3(prime) DNA-binding domain

Domain ID domain_id	2dwmD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily	60 — PriA, 3(prime) DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	112.660 Å
Unit-cell length b length_b	112.660 Å
Unit-cell length c length_c	260.720 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	72

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2708
R_free r_free	0.3177

Description description	5'-D(APT)-3'
Molecular weight formula_weight	572.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G
Atom count atom_count	3374

Crystal structure of the PriA protein complexed with oligonucleotides

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

Primosomal protein N

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/dw/2dwm/2dwm.fit
pddf	/app/data/pr_computation/dw/2dwm/2dwm.pr.out
profile	/app/data/saxs_computation/dw/2dwm/2dwm.dat