SAXSdb — 7t21

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

Replicative DNA helicase

Escherichia coli K-12

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 × 6 DNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain A； UniProt 1–471 Chain B； UniProt 1–471 Chain C； UniProt 1–471 Chain D； UniProt 1–471 Chain E； UniProt 1–471 Chain F； UniProt 1–471	Not recorded	;DNA (5'-D(TPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3') ; × 1 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

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 7T21	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B79 N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB Deposited 1999-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–129（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	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
1B79 N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB Deposited 1999-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–129（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	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
1B79 N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB Deposited 1999-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 16–129（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	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
1B79 N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB Deposited 1999-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 16–129（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	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
1JWE NMR Structure of the N-Terminal Domain of E. Coli Dnab Helicase Deposited 1999-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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
7T22 E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2021-12-02	Different mutation/modification Different oligomeric state 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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 12 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 1–471； UniProt 1–471 Author chain B； PDBConstruct 1–471； UniProt 1–471 Author chain C； PDBConstruct 1–471； UniProt 1–471 Author chain D； PDBConstruct 1–471； UniProt 1–471 Author chain E； PDBConstruct 1–471； UniProt 1–471 Author chain F； PDBConstruct 1–471； UniProt 1–471

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	7t21
Deposition date deposition_date	2021-12-02
Structure title title	E. coli DnaB bound to ssDNA and ADP-AlF4
Keywords keywords	helicase, SF4, AAA+, REPLICATION-DNA complex; REPLICATION/DNA
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	45.16 Å
Radius of gyration Rg (electron density) rg_electron	44.63 Å
Forward intensity I(0) i0	1482560000.00
Molecular weight molecular_weight	305660.0 kDa
Excluded volume excluded_volume	377260 Å³
Envelope volume envelope_volume	528570 Å³
Hydration-shell volume shell_volume	94079 Å³
Envelope diameter envelope_diameter	151.0 Å
Shell Rg shell_rg	53.49 Å
Envelope Rg envelope_rg	43.42 Å
Shape Rg shape_rg	44.69 Å
Total Rg total_rg	44.79 Å
Total atoms total_atoms	21425
Residues n_residues	2701
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	139.5 Å
Rg (real space) rg_real	44.85 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.4830e+09
I(0) uncertainty (real space) i0_real_error	2.3390e+07
Rg (reciprocal space) rg_reciprocal	45.16 Å
I(0) (reciprocal space) i0_reciprocal	1483000000.0000
Solution quality estimate total_estimate	0.6654
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.8 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.496
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	170200000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.971; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Replicative DNA helicase
Molecular weight formula_weight	52450.9 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21425

MAGNKPFNKQQAEPRERDPQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRERAVVREMISVANEIAEAGFDPQGRTSEDLLDLAESRVFKIAESRANKDEGPKNIADVLDATVARIEQLFQQPHDGVTGVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLVENAAMLQDKPVLIFSLEMPSEQIMMRSLASLSRVDQTKIRTGQLDDEDWARISGTMGILLEKRNIYIDDSSGLTPTEVRSRARRIAREHGGIGLIMIDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGPQYDDE

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3') ;
Molecular weight formula_weight	6038.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

TTTTTTTTTTTTTTTTTTTT

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	TETRAFLUOROALUMINATE ION
Molecular weight formula_weight	103.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	5.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	98118

fit	/app/data/saxs_computation/t2/7t21/7t21.fit
pddf	/app/data/pr_computation/t2/7t21/7t21.pr.out
profile	/app/data/saxs_computation/t2/7t21/7t21.dat

E. coli DnaB bound to ssDNA and ADP-AlF4

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

Replicative DNA 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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)