SAXSdb — 4ou6

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

Primosomal protein 1

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 × 5 DNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 84–159 Chain B； UniProt 84–159 Chain C； UniProt 84–159 Chain D； UniProt 84–159 Chain E； UniProt 84–159	Fragment：UNP RESIDUES 84-159	;DNA (5'-D(PTPTPTPTPTPTPTPTPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.96 Å R-free 0.228

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 4OU6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RU8 DnaT C-terminal domain Deposited 2014-01-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 89–179（91 aa） Fragment：ssDNA binding domain, UNP residues 89-179	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] DnaT-1, 20 mM HEPES-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1 mM [U-99% 15N] DnaT-3, 20 mM HEPES-4, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4OU7 Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode Deposited 2014-02-15	Different construct Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 5 PDB declaration: hexameric	Chain A 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain B 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain C 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain D 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain E 84–154（71 aa） Fragment：UNP RESIDUES 84-154	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.83 Å R-free 0.238
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 D 1–179（179 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 C 1–154（154 aa） Chain D 1–154（154 aa） Chain E 1–154（154 aa） Chain T 1–154（154 aa） Chain W 1–154（154 aa） Chain X 1–154（154 aa） Chain Y 1–154（154 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNAT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 84–159 Author chain B； PDBConstruct 1–76； UniProt 84–159 Author chain C； PDBConstruct 1–76； UniProt 84–159 Author chain D； PDBConstruct 1–76； UniProt 84–159 Author chain E； PDBConstruct 1–76； UniProt 84–159

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	4ou6
Deposition date deposition_date	2014-02-15
Structure title title	Crystal structure of DnaT84-153-dT10 ssDNA complex form 1
Keywords keywords	DNA binding, REPLICATION-DNA complex; REPLICATION/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	25.68 Å
Radius of gyration Rg (electron density) rg_electron	25.10 Å
Forward intensity I(0) i0	32491300.00
Molecular weight molecular_weight	44115.0 kDa
Excluded volume excluded_volume	55145 Å³
Envelope volume envelope_volume	70676 Å³
Hydration-shell volume shell_volume	23728 Å³
Envelope diameter envelope_diameter	86.5 Å
Shell Rg shell_rg	32.03 Å
Envelope Rg envelope_rg	24.70 Å
Shape Rg shape_rg	25.09 Å
Total Rg total_rg	25.95 Å
Total atoms total_atoms	3115
Residues n_residues	369
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	82.1 Å
Rg (real space) rg_real	25.65 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.2490e+07
I(0) uncertainty (real space) i0_real_error	4.4310e+05
Rg (reciprocal space) rg_reciprocal	25.66 Å
I(0) (reciprocal space) i0_reciprocal	32490000.0000
Solution quality estimate total_estimate	0.6984
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.595
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22370000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 0.164; Positv: 1.000; Valcen: 0.983; Smooth: 0.820

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Primosomal protein 1
Molecular weight formula_weight	8606.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3372

VPMGKFAMYPDWQPDADFIRLAALWGVALREPVTTEELASFIAYWQAEGKVFHHVQWQQKLARSLQIGRASNGGLP

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPTPTPTPTPT)-3') ;
Molecular weight formula_weight	2997.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

TTTTTTTTTT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	257

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8. Citations (1)

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Unit-cell length a length_a	47.144 Å
Unit-cell length b length_b	47.416 Å
Unit-cell length c length_c	54.135 Å
Unit-cell angle α angle_alpha	88.34 °
Unit-cell angle β angle_beta	86.25 °
Unit-cell angle γ angle_gamma	71.24 °
Molecules per unit cell Z z_pdb	5

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

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	27.540 Å
R factor r_factor	0.1906
R_work r_work	0.1886
R_free r_free	0.2285

fit	/app/data/saxs_computation/ou/4ou6/4ou6.fit
pddf	/app/data/pr_computation/ou/4ou6/4ou6.pr.out
profile	/app/data/saxs_computation/ou/4ou6/4ou6.dat

Crystal structure of DnaT84-153-dT10 ssDNA complex form 1

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

Primosomal protein 1

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)