SAXSdb — 1b79

▼

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

DnaB Helicase

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 16–129	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；pH 6.9, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.293
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 16–129	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；pH 6.9, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.293
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 16–129	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；pH 6.9, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.293
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 16–129	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；pH 6.9, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.293

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 1B79	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JWE NMR Structure of the N-Terminal Domain of E. Coli Dnab Helicase Deposited 1999-01-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–137（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；305 K；Ionic strength (raw mmCIF value) 20 mM；Pressure 1	Resolution not provided
6QEM E. coli DnaBC complex bound to ssDNA Deposited 2019-01-08	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 × 12 PDB declaration: tridecameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7T20 E. coli DnaB bound to ssDNA and AMPPNP Deposited 2021-12-02	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 Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 4.70 Å
7T21 E. coli DnaB bound to ssDNA and ADP-AlF4 Deposited 2021-12-02	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 Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 5.40 Å
7T22 E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2021-12-02	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 × 9 PDB declaration: decameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C	ADP ADENOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 4.20 Å
8V9T Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio Deposited 2023-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 2.84 Å
9ECO E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2024-11-14	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 × 8 PDB declaration: nonameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C Mutation：F103C	ALF TETRAFLUOROALUMINATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP, 0.5 mM AlCl3, 5 mM NaF. cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.	Resolution 2.83 Å
9OA1 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio. Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 2.66 Å
9OA2 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio. Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa） Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM), ssDNA (1.875 uM), and LO-156-299-NHis (2.25 uM) was mixed at 1.25 and 1.5 molar excess, respectively. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 3.85 Å

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

View Construct and Data Evidence

UniProt name	DNAB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–119； UniProt 16–129 Author chain B； PDBConstruct 6–119； UniProt 16–129 Author chain C； PDBConstruct 6–119； UniProt 16–129 Author chain D； PDBConstruct 6–119； UniProt 16–129

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b79
Deposition date deposition_date	1999-01-28
Structure title title	N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB
Keywords keywords	HELICASE, HEXAMER, DNA REPLICATION, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.31 Å
Radius of gyration Rg (electron density) rg_electron	30.02 Å
Forward intensity I(0) i0	37006700.00
Molecular weight molecular_weight	45408.0 kDa
Excluded volume excluded_volume	55996 Å³
Envelope volume envelope_volume	74068 Å³
Hydration-shell volume shell_volume	22558 Å³
Envelope diameter envelope_diameter	101.9 Å
Shell Rg shell_rg	34.05 Å
Envelope Rg envelope_rg	29.57 Å
Shape Rg shape_rg	30.01 Å
Total Rg total_rg	30.43 Å
Total atoms total_atoms	3202
Residues n_residues	410
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

▼

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

Maximum dimension Dmax dmax	98.5 Å
Rg (real space) rg_real	30.38 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	3.7010e+07
I(0) uncertainty (real space) i0_real_error	5.7970e+05
Rg (reciprocal space) rg_reciprocal	30.36 Å
I(0) (reciprocal space) i0_reciprocal	37010000.0000
Solution quality estimate total_estimate	0.8601
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	43.6 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5511000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.855

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b79a_
Class class	a — All alpha proteins
Fold Fold fold	a.81 — N-terminal domain of DnaB helicase
Superfamily Superfamily superfamily	a.81.1 — N-terminal domain of DnaB helicase
Family Family family	a.81.1.1 — N-terminal domain of DnaB helicase

Domain ID domain_id	d1b79b_
Class class	a — All alpha proteins
Fold Fold fold	a.81 — N-terminal domain of DnaB helicase
Superfamily Superfamily superfamily	a.81.1 — N-terminal domain of DnaB helicase
Family Family family	a.81.1.1 — N-terminal domain of DnaB helicase

Domain ID domain_id	d1b79c_
Class class	a — All alpha proteins
Fold Fold fold	a.81 — N-terminal domain of DnaB helicase
Superfamily Superfamily superfamily	a.81.1 — N-terminal domain of DnaB helicase
Family Family family	a.81.1.1 — N-terminal domain of DnaB helicase

Domain ID domain_id	d1b79d_
Class class	a — All alpha proteins
Fold Fold fold	a.81 — N-terminal domain of DnaB helicase
Superfamily Superfamily superfamily	a.81.1 — N-terminal domain of DnaB helicase
Family Family family	a.81.1.1 — N-terminal domain of DnaB helicase

CATH v4.4 (4 domains)

Domain ID domain_id	1b79A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	1b79B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	1b79C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	1b79D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

▶

8. Citations (1)

▶

Unit-cell length a length_a	35.300 Å
Unit-cell length b length_b	66.400 Å
Unit-cell length c length_c	107.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2630
R_free r_free	0.2930

Description description	DnaB Helicase
Molecular weight formula_weight	13222.7 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3245

N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB

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

DnaB Helicase

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

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

fit	/app/data/saxs_computation/b7/1b79/1b79.fit
pddf	/app/data/pr_computation/b7/1b79/1b79.pr.out
profile	/app/data/saxs_computation/b7/1b79/1b79.dat