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2r6d

Crystal Form B1

Method: X-RAY DIFFRACTION Dmax: 144.5 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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） 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 No other associated polymer 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

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 2R6D 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
2R6E Crystal Form B2 Deposited 2007-09-05 Different construct Different mutation/modification 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

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 2r6d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2r6d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2r6d
Deposition date deposition_date2007-09-05
Structure title titleCrystal Form B1
Keywords keywordsHelicase, Replication DnaB, Hexameric, 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_guinier47.14 Å
Radius of gyration Rg (electron density) rg_electron46.38 Å
Forward intensity I(0) i0961536000.00
Molecular weight molecular_weight257710.0 kDa
Excluded volume excluded_volume323530 ų
Envelope volume envelope_volume492400 ų
Hydration-shell volume shell_volume86245 ų
Envelope diameter envelope_diameter149.6 Å
Shell Rg shell_rg54.59 Å
Envelope Rg envelope_rg43.84 Å
Shape Rg shape_rg46.40 Å
Total Rg total_rg46.65 Å
Total atoms total_atoms18085
Residues n_residues2340
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 dmax144.5 Å
Rg (real space) rg_real46.74 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real9.6150e+08
I(0) uncertainty (real space) i0_real_error1.5290e+07
Rg (reciprocal space) rg_reciprocal47.14 Å
I(0) (reciprocal space) i0_reciprocal962000000.0000
Solution quality estimate total_estimate0.8940
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary65.7 Å
Skewness Skewness skewness-0.041
Kurtosis Kurtosis kurtosis-0.603
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha77080000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.921
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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) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id2r6dA01
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_id2r6dA02
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_id2r6dB01
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_id2r6dB02
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_id2r6dC01
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_id2r6dC02
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_id2r6dD01
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_id2r6dD02
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_id2r6dE01
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_id2r6dE02
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_id2r6dF01
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_id2r6dF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)