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1t3w

Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)

Method: X-RAY DIFFRACTION Dmax: 85.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA primase

Escherichia coli

UniProt P0ABS5

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 434–581 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.80 Å R-free 0.308
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 434–581 Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.80 Å R-free 0.308
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 434–581 Chain B； UniProt 434–581 Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.80 Å R-free 0.308

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 1T3W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DD9 STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN
Not recorded SR STRONTIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM SRCL2, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.276
1DDE STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN
Not recorded Y1 YTTRIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM YCL2, VAPOR DIFFUSION, HANGING DROP
Resolution 1.70 Å R-free 0.263
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
2HAJ Solution structure of the helicase-binding domain of Escherichia coli primase Deposited 2006-06-13 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：Helicase-binding domain, residues 447-581
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR sample composition 0.3mM DnaG-C U-15N, 13C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3mM DnaG-C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
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 G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Chain I 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C Mutation：R568C 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
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 G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C 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

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

View Construct and Data Evidence
UniProt name PRIM_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–148； UniProt 434–581 Author chain B； PDBConstruct 1–148； UniProt 434–581

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 1t3w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t3w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t3w
Deposition date deposition_date2004-04-28
Structure title titleCrystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)
Keywords keywordsDnaG, DNA-directed RNA polymerase, E. coli, DNA replication, REPLICATION; REPLICATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.34 Å
Radius of gyration Rg (electron density) rg_electron25.41 Å
Forward intensity I(0) i017443700.00
Molecular weight molecular_weight30987.0 kDa
Excluded volume excluded_volume38477 ų
Envelope volume envelope_volume52459 ų
Hydration-shell volume shell_volume18591 ų
Envelope diameter envelope_diameter85.6 Å
Shell Rg shell_rg30.05 Å
Envelope Rg envelope_rg25.44 Å
Shape Rg shape_rg25.46 Å
Total Rg total_rg25.83 Å
Total atoms total_atoms2157
Residues n_residues263
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 dmax85.0 Å
Rg (real space) rg_real26.45 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real1.7440e+07
I(0) uncertainty (real space) i0_real_error2.8330e+05
Rg (reciprocal space) rg_reciprocal26.42 Å
I(0) (reciprocal space) i0_reciprocal17440000.0000
Solution quality estimate total_estimate0.8790
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.7 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.610
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2721000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.819; Smooth: 0.873
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1t3wa_
Class classa — All alpha proteins
Fold Fold folda.236 — DNA primase DnaG, C-terminal domain
Superfamily Superfamily superfamilya.236.1 — DNA primase DnaG, C-terminal domain
Family Family familya.236.1.1 — DNA primase DnaG, C-terminal domain
Domain ID domain_idd1t3wb_
Class classa — All alpha proteins
Fold Fold folda.236 — DNA primase DnaG, C-terminal domain
Superfamily Superfamily superfamilya.236.1 — DNA primase DnaG, C-terminal domain
Family Family familya.236.1.1 — DNA primase DnaG, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id1t3wA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily10 — DNAb Helicase; Chain A
Domain ID domain_id1t3wB00
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 (2)

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9. Files and Curves (10)