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2r6c

Crystal Form BH2

Method: X-RAY DIFFRACTION Dmax: 157.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Replicative helicase

Bacillus 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 × 18 PDB declaration: octadecameric（18） 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 DnaG Primase, Helicase Binding Domain × 6 （Q9X4D0） 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

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 2R6C 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
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
4M4W Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex Deposited 2013-08-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
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 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

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

View Construct and Data Evidence
UniProt name Q9X4C9_BACST
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

DnaG Primase, Helicase Binding Domain

Bacillus 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 × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain G； UniProt 455–597 Chain H； UniProt 455–597 Chain I； UniProt 455–597 Fragment：Helicase Binding Domain Non-standard monomer：Yes (specific site not provided by mmCIF) Replicative helicase × 12 （Q9X4C9） 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

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 2R6C 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
4M4W Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex Deposited 2013-08-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
Chain H 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
Chain I 455–597（143 aa） Fragment：Helicase Binding Domain (UNP residues 455-597)
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 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

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

View Construct and Data Evidence
UniProt name PRIM_BACST
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

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 2r6c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2r6c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2r6c
Deposition date deposition_date2007-09-05
Structure title titleCrystal Form BH2
Keywords keywordsHelicase, Primase, Replication, dnaB, dnaG; 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_guinier52.14 Å
Radius of gyration Rg (electron density) rg_electron51.45 Å
Forward intensity I(0) i01156420000.00
Molecular weight molecular_weight284670.0 kDa
Excluded volume excluded_volume357140 ų
Envelope volume envelope_volume568730 ų
Hydration-shell volume shell_volume90552 ų
Envelope diameter envelope_diameter155.5 Å
Shell Rg shell_rg58.35 Å
Envelope Rg envelope_rg48.70 Å
Shape Rg shape_rg51.42 Å
Total Rg total_rg51.80 Å
Total atoms total_atoms19920
Residues n_residues2544
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 dmax157.7 Å
Rg (real space) rg_real51.86 Å
Rg uncertainty (real space) rg_real_error1.26 Å
I(0) (real space) i0_real1.1560e+09
I(0) uncertainty (real space) i0_real_error2.1690e+07
Rg (reciprocal space) rg_reciprocal52.36 Å
I(0) (reciprocal space) i0_reciprocal1157000000.0000
Solution quality estimate total_estimate0.8332
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary73.6 Å
Skewness Skewness skewness-0.037
Kurtosis Kurtosis kurtosis-0.640
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha75310000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id2r6cA01
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_id2r6cA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cB01
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_id2r6cB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cC01
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_id2r6cC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cD01
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_id2r6cD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cE01
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_id2r6cE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cF01
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_id2r6cF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2r6cG01
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_id2r6cG02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily360 —
Domain ID domain_id2r6cH01
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_id2r6cH02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily360 —
Domain ID domain_id2r6cI01
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_id2r6cI02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily360 —
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8. Citations (1)

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9. Files and Curves (10)