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4m4w

Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex

Method: X-RAY DIFFRACTION Dmax: 179.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Replicative helicase

Geobacillus stearothermophilus

UniProt Q9X4C9

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain A； UniProt 1–454 Chain B； UniProt 1–454 Chain C； UniProt 1–454 Chain D； UniProt 1–454 Chain E； UniProt 1–454 Chain F； UniProt 1–454 Not recorded DNA primase × 3 （Q9X4D0） Primosomal protein DnaI × 6 （P06567） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；290 K；11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K Resolution 6.10 Å R-free 0.392

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 4M4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2R6A Crystal Form BH1 Deposited 2007-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–454（454 aa）
Chain B 1–454（454 aa）
Not recorded SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.0M Lithium Sulfate, 5% MPD, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.90 Å R-free 0.297
2R6C Crystal Form BH2 Deposited 2007-09-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–454（454 aa）
Chain B 1–454（454 aa）
Chain C 1–454（454 aa）
Chain D 1–454（454 aa）
Chain E 1–454（454 aa）
Chain F 1–454（454 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.5M Sodium Succinate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 4.00 Å R-free 0.344
2R6D Crystal Form B1 Deposited 2007-09-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Chain B 1–454（454 aa）
Chain C 1–454（454 aa）
Chain D 1–454（454 aa）
Chain E 1–454（454 aa）
Chain F 1–454（454 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；1.0M Ammonium Acetate, pH 5.5, VAPOR DIFFUSION, temperature 298K
Resolution 3.70 Å R-free 0.322
2R6E Crystal Form B2 Deposited 2007-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–454（454 aa）
Chain B 1–454（454 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；2.5M Sodium Chloride, pH 7.0, VAPOR DIFFUSION
Resolution 5.02 Å R-free 0.397
4ESV A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates Deposited 2012-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 1–454（454 aa）
Chain B 1–454（454 aa）
Chain C 1–454（454 aa）
Chain D 1–454（454 aa）
Chain E 1–454（454 aa）
Chain F 1–454（454 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CA CALCIUM ION × 11 GDP GUANOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；4-7% PEG3350, 0.2 M calcium chloride, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 3.20 Å R-free 0.289
4ESV A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates Deposited 2012-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain G 1–454（454 aa）
Chain H 1–454（454 aa）
Chain I 1–454（454 aa）
Chain J 1–454（454 aa）
Chain K 1–454（454 aa）
Chain L 1–454（454 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CA CALCIUM ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；4-7% PEG3350, 0.2 M calcium chloride, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 3.20 Å R-free 0.289

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9X4C9_GEOSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–454； UniProt 1–454 Author chain B； PDBConstruct 1–454； UniProt 1–454 Author chain C； PDBConstruct 1–454； UniProt 1–454 Author chain D； PDBConstruct 1–454； UniProt 1–454 Author chain E； PDBConstruct 1–454； UniProt 1–454 Author chain F； PDBConstruct 1–454； UniProt 1–454

DNA primase

Geobacillus stearothermophilus

UniProt Q9X4D0

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain G； UniProt 455–597 Chain H； UniProt 455–597 Chain I； UniProt 455–597 Fragment：Helicase Binding Domain (UNP residues 455-597) Non-standard monomer：Yes (specific site not provided by mmCIF) Replicative helicase × 6 （Q9X4C9） Primosomal protein DnaI × 6 （P06567） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；290 K；11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K Resolution 6.10 Å R-free 0.392

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 4M4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0Q STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE Deposited 1999-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–103（103 aa） Fragment：ZINC-BINDING DOMAIN
Chain B 1–103（103 aa） Fragment：ZINC-BINDING DOMAIN
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；LITHIUM SULFATE, SODIUM CITRATE, ZINC ACETATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.71 Å R-free 0.225
1Z8S DnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597) Deposited 2005-03-31 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 451–597（147 aa） Fragment：P16, Residues 451-597
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 200mM sodium chloride；Pressure ambient
NMR sample composition 1mM U-15N P16 | 90% H2O/10% D2O
NMR sample composition 1mM U-15N U13C P16 | 90% H2O/10% D2O
NMR sample composition 0.5mM U-15N P16 | 50% H2O/50% D2O
Resolution not provided
2R6A Crystal Form BH1 Deposited 2007-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 455–597（143 aa） Fragment：Helicase Binding Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.0M Lithium Sulfate, 5% MPD, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.90 Å R-free 0.297
2R6C Crystal Form BH2 Deposited 2007-09-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain G 455–597（143 aa） Fragment：Helicase Binding Domain
Chain H 455–597（143 aa） Fragment：Helicase Binding Domain
Chain I 455–597（143 aa） Fragment：Helicase Binding Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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；pH 6.5；298 K；0.5M Sodium Succinate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 4.00 Å R-free 0.344

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

View Construct and Data Evidence
UniProt name PRIM_GEOSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–143； UniProt 455–597 Author chain H； PDBConstruct 1–143； UniProt 455–597 Author chain I； PDBConstruct 1–143； UniProt 455–597

Primosomal protein DnaI

Bacillus subtilis subsp. subtilis

UniProt P06567

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain J； UniProt 1–311 Chain K； UniProt 1–311 Chain L； UniProt 1–311 Chain M； UniProt 1–311 Chain N； UniProt 1–311 Chain O； UniProt 1–311 Not recorded Replicative helicase × 6 （Q9X4C9） DNA primase × 3 （Q9X4D0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；290 K；11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K Resolution 6.10 Å R-free 0.392

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 4M4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2K7R N-terminal domain of the Bacillus subtilis helicase-loading protein DnaI Deposited 2008-08-19 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 1–106（106 aa） Fragment：UNP residues 1-106
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.5mM [U-95% 15N] DnaI, 0.5mM zinc ion, 10% [U-99% 2H] D2O, 90% H2O, 10mM sodium phosphate, 0.1% sodium azide, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNAI_BACSU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J； PDBConstruct 1–311； UniProt 1–311 Author chain K； PDBConstruct 1–311； UniProt 1–311 Author chain L； PDBConstruct 1–311； UniProt 1–311 Author chain M； PDBConstruct 1–311； UniProt 1–311 Author chain N； PDBConstruct 1–311； UniProt 1–311 Author chain O； PDBConstruct 1–311； UniProt 1–311

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 4m4w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4m4w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4m4w
Deposition date deposition_date2013-08-07
Structure title titleMechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex
Keywords keywordsprimase, helicase loader, DnaB, DnaG, DnaI, 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_guinier59.80 Å
Radius of gyration Rg (electron density) rg_electron58.96 Å
Forward intensity I(0) i02904450000.00
Molecular weight molecular_weight456340.0 kDa
Excluded volume excluded_volume573030 ų
Envelope volume envelope_volume1016300 ų
Hydration-shell volume shell_volume142600 ų
Envelope diameter envelope_diameter183.0 Å
Shell Rg shell_rg65.35 Å
Envelope Rg envelope_rg55.21 Å
Shape Rg shape_rg58.95 Å
Total Rg total_rg59.17 Å
Total atoms total_atoms31981
Residues n_residues4025
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 dmax179.9 Å
Rg (real space) rg_real59.31 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real2.9040e+09
I(0) uncertainty (real space) i0_real_error5.3710e+07
Rg (reciprocal space) rg_reciprocal60.20 Å
I(0) (reciprocal space) i0_reciprocal2909000000.0000
Solution quality estimate total_estimate0.8408
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary83.0 Å
Skewness Skewness skewness-0.025
Kurtosis Kurtosis kurtosis-0.420
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha330000000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.408
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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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8. Citations (1)

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9. Files and Curves (10)