4esv

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

Method: X-RAY DIFFRACTION D_max: 213.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Replicative helicase

Geobacillus stearothermophilus

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–DNA Homooligomer Protein × 6 DNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	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	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3' × 1 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
2	Protein–DNA Homooligomer Protein × 6 DNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain G； UniProt 1–454 Chain H； UniProt 1–454 Chain I； UniProt 1–454 Chain J； UniProt 1–454 Chain K； UniProt 1–454 Chain L； UniProt 1–454	Not recorded	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPT)-3' × 1 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

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 4ESV	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 ligand/ion 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 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） 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
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 ligand/ion 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9X4C9_GEOSE
Isoform	—
PDB entities	3
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 Author chain G； PDBConstruct 1–454； UniProt 1–454 Author chain H； PDBConstruct 1–445； UniProt 1–454 Author chain I； PDBConstruct 1–454； UniProt 1–454 Author chain J； PDBConstruct 1–454； UniProt 1–454 Author chain K； PDBConstruct 1–454； UniProt 1–454 Author chain L； 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4esv
Deposition date deposition_date	2012-04-23
Structure title title	A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates
Keywords keywords	RecA Fold, Helicase, HYDROLASE-DNA complex; HYDROLASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	75.59 Å
Radius of gyration Rg (electron density) rg_electron	75.85 Å
Forward intensity I(0) i0	4828710000.00
Molecular weight molecular_weight	575470.0 kDa
Excluded volume excluded_volume	715270 Å³
Envelope volume envelope_volume	1167000 Å³
Hydration-shell volume shell_volume	128320 Å³
Envelope diameter envelope_diameter	248.1 Å
Shell Rg shell_rg	74.72 Å
Envelope Rg envelope_rg	72.00 Å
Shape Rg shape_rg	75.85 Å
Total Rg total_rg	75.84 Å
Total atoms total_atoms	40283
Residues n_residues	5099
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	213.3 Å
Rg (real space) rg_real	75.71 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	4.8250e+09
I(0) uncertainty (real space) i0_real_error	8.0690e+07
Rg (reciprocal space) rg_reciprocal	74.34 Å
I(0) (reciprocal space) i0_reciprocal	4813000000.0000
Solution quality estimate total_estimate	0.8069
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.9 Å
Skewness Skewness skewness	0.260
Kurtosis Kurtosis kurtosis	-0.979
Angular range angular_range	— – 0.1050 Å⁻¹
Current regularization parameter α current_alpha	0.0037
Highest regularization parameter α highest_alpha	388300000.0000
Real-space data points n_real_points	22
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3'
Molecular weight formula_weight	4213.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	V
Atom count atom_count	40296

TTTTTTTTTTTTTT

Entity 2 Entity 2 polymer

Description description	5'-D(PTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'
Molecular weight formula_weight	3909.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W

TTTTTTTTTTTTT

Entity 3 Entity 3 polymer

Description description	Replicative helicase
Molecular weight formula_weight	50699.4 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L

MSELFSERIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNLERRFDEAQIPPGA

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 7 Entity 7 non-polymer

Description description	TETRAFLUOROALUMINATE ION
Molecular weight formula_weight	103.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	4esvA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4esvL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	4esvL02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	149.124 Å
Unit-cell length b length_b	180.321 Å
Unit-cell length c length_c	279.128 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	47.920 Å
R factor r_factor	0.2450
R_work r_work	0.2420
R_free r_free	0.2890

fit	/app/data/saxs_computation/es/4esv/4esv.fit
pddf	/app/data/pr_computation/es/4esv/4esv.pr.out
profile	/app/data/saxs_computation/es/4esv/4esv.dat

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

1. Protein Identity and Related Structures Protein Identity & Related Structures

Replicative helicase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)