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1jwe

NMR Structure of the N-Terminal Domain of E. Coli Dnab Helicase

Method: SOLUTION NMR Dmax: 48.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (DNAB HELICASE)

Escherichia coli

UniProt P0ACB0

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 24–137 Fragment：N-TERMINAL DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.5；305 K；Ionic strength (raw mmCIF value) 20 mM；Pressure 1 Resolution not provided

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 1JWE 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 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 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 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 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
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 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 1–114； UniProt 24–137

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1jwe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jwe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jwe
Deposition date deposition_date1999-01-22
Structure title titleNMR Structure of the N-Terminal Domain of E. Coli Dnab Helicase
Keywords keywordsHELICASE, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.95 Å
Radius of gyration Rg (electron density) rg_electron13.68 Å
Forward intensity I(0) i0960330000.00
Molecular weight molecular_weight253860.0 kDa
Excluded volume excluded_volume314070 ų
Envelope volume envelope_volume28151 ų
Hydration-shell volume shell_volume14939 ų
Envelope diameter envelope_diameter55.7 Å
Shell Rg shell_rg22.01 Å
Envelope Rg envelope_rg16.62 Å
Shape Rg shape_rg13.62 Å
Total Rg total_rg14.04 Å
Total atoms total_atoms35300
Residues n_residues2280
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax48.5 Å
Rg (real space) rg_real13.90 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real9.6030e+08
I(0) uncertainty (real space) i0_real_error1.1040e+07
Rg (reciprocal space) rg_reciprocal13.90 Å
I(0) (reciprocal space) i0_reciprocal960300000.0000
Solution quality estimate total_estimate0.8544
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.180
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha342400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.972
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1jwea_
Class classa — All alpha proteins
Fold Fold folda.81 — N-terminal domain of DnaB helicase
Superfamily Superfamily superfamilya.81.1 — N-terminal domain of DnaB helicase
Family Family familya.81.1.1 — N-terminal domain of DnaB helicase

CATH v4.4 (1 domains)

Domain ID domain_id1jweA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily10 — DNAb Helicase; Chain A
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8. Citations (1)

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9. Files and Curves (10)