SAXSdb — 6bbm

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

Replicative DNA helicase

Escherichia coli O111:NM

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain A； UniProt 1–471 Chain B； UniProt 1–471 Chain C； UniProt 1–471 Chain D； UniProt 1–471 Chain E； UniProt 1–471 Chain F； UniProt 1–471	Not recorded	Replication protein P × 5 （P03689） ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation. cryo-EM vitrification conditions：Cryogen ETHANE；3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.	Resolution 4.10 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A365Q7M1_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 1–471 Author chain B； PDBConstruct 1–471； UniProt 1–471 Author chain C； PDBConstruct 1–471； UniProt 1–471 Author chain D； PDBConstruct 1–471； UniProt 1–471 Author chain E； PDBConstruct 1–471； UniProt 1–471 Author chain F； PDBConstruct 1–471； UniProt 1–471

Replication protein P

Escherichia phage lambda

UniProt P03689

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain V； UniProt 1–107 Chain W； UniProt 1–107 Chain X； UniProt 1–107 Chain Y； UniProt 1–107 Chain Z； UniProt 1–107	Not recorded	Replicative DNA helicase × 6 （A0A365Q7M1） ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation. cryo-EM vitrification conditions：Cryogen ETHANE；3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.	Resolution 4.10 Å

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 6BBM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8V9S Distinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage Lambda P Helicase Loader Deposited 2023-12-09	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 105–210（106 aa） Fragment：residues 105 to 210	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, SITTING DROP；298.15 K；Crystals were prepared using the sitting drop vapor diffusion method by mixing either 0.1, or 0.2, or 0.4 uL of the protein solution and 0.2 uL of a series of commercially available crystallization screens (Qiagen). Optimized crystals for X-ray diffraction were grown at room temperature in a buffer consisting of 3 M to 4 M NaCl with 0.1 M HEPES-NaOH, pH 7 to 8 and required 7 days to form.	Resolution 1.86 Å R-free 0.244
8V9T Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio Deposited 2023-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain V 1–233（233 aa） Chain W 1–233（233 aa） Chain X 1–233（233 aa） Chain Y 1–233（233 aa） Chain Z 1–233（233 aa）	Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 2.84 Å
9OA1 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio. Deposited 2025-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain V 1–233（233 aa） Chain W 1–233（233 aa） Chain X 1–233（233 aa） Chain Y 1–233（233 aa） Chain Z 1–233（233 aa）	Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 2.66 Å
9OA2 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio. Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain U 1–233（233 aa） Chain V 1–233（233 aa） Chain W 1–233（233 aa） Chain X 1–233（233 aa） Chain Y 1–233（233 aa） Chain Z 1–233（233 aa）	Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM), ssDNA (1.875 uM), and LO-156-299-NHis (2.25 uM) was mixed at 1.25 and 1.5 molar excess, respectively. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	Resolution 3.85 Å

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

View Construct and Data Evidence

UniProt name	VRPP_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain V； PDBConstruct 1–107； UniProt 1–107 Author chain W； PDBConstruct 1–107； UniProt 1–107 Author chain X； PDBConstruct 1–107； UniProt 1–107 Author chain Y； PDBConstruct 1–107； UniProt 1–107 Author chain Z； PDBConstruct 1–107； UniProt 1–107

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6bbm
Deposition date deposition_date	2017-10-18
Structure title title	Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex
Keywords keywords	Helicase Loader, Helicase, DNA replication, ATPase, DNA Replication Initiation, Bacteriophage Lambda, REPLICATION; REPLICATION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	47.13 Å
Radius of gyration Rg (electron density) rg_electron	46.33 Å
Forward intensity I(0) i0	1872620000.00
Molecular weight molecular_weight	340530.0 kDa
Excluded volume excluded_volume	418340 Å³
Envelope volume envelope_volume	621340 Å³
Hydration-shell volume shell_volume	105070 Å³
Envelope diameter envelope_diameter	152.8 Å
Shell Rg shell_rg	55.62 Å
Envelope Rg envelope_rg	45.96 Å
Shape Rg shape_rg	46.39 Å
Total Rg total_rg	46.45 Å
Total atoms total_atoms	23956
Residues n_residues	3280
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	150.7 Å
Rg (real space) rg_real	46.83 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.8730e+09
I(0) uncertainty (real space) i0_real_error	3.4780e+07
Rg (reciprocal space) rg_reciprocal	47.13 Å
I(0) (reciprocal space) i0_reciprocal	1873000000.0000
Solution quality estimate total_estimate	0.8852
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.4 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.467
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	316500000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.892

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Replicative DNA helicase
Molecular weight formula_weight	52450.9 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23956

MAGNKPFNKQQAEPRERDPQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRERAVVREMISVANEIAEAGFDPQGRTSEDLLDLAESRVFKIAESRANKDEGPKNIADVLDATVARIEQLFQQPHDGVTGVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLVENAAMLQDKPVLIFSLEMPSEQIMMRSLASLSRVDQTKIRTGQLDDEDWARISGTMGILLEKRNIYIDDSSGLTPTEVRSRARRIAREHGGIGLIMIDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGPQYDDE

来源 Source

来源生物 organism	Escherichia coli O111:NM
NCBI Class编号 ncbi_taxonomy_id	373045
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Replication protein P
Molecular weight formula_weight	23141.2 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,W,X,Y,Z

MKNIAAQMVNFDREQMRRIANNMPEQYDEKPQVQQVAQIINGVFSQLLATFPASLANRDQNEVNEIRRQWVLAFRENGITTMEQVNAGMRVARRQNRPFLPSPGQFVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

来源 Source

来源生物 organism	Escherichia phage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	5

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	90883

fit	/app/data/saxs_computation/bb/6bbm/6bbm.fit
pddf	/app/data/pr_computation/bb/6bbm/6bbm.pr.out
profile	/app/data/saxs_computation/bb/6bbm/6bbm.dat

Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

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

Replicative DNA helicase

State in the Current Structure

Other States of the Same Protein in the Database

Replication protein P

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)