SAXSdb — 6vsx

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

DNA helicase

Bacillus subtilis

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 608–774	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.2；300 K；0.1M Na/K phosphate, pH 6.2, 0.2 M NaCl, 50 % PEG200	Resolution 2.00 Å R-free 0.202

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 6VSX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ZCA Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) Deposited 2020-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 1–774（774 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6ZFB Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) Deposited 2020-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–774（774 aa） Chain h 1–774（774 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A164TSE8_BACIU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–188； UniProt 608–774

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	6vsx
Deposition date deposition_date	2020-02-12
Structure title title	X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD
Keywords keywords	RNA polymerase, Helicase, TRANSCRIPTION; TRANSCRIPTION
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	16.04 Å
Radius of gyration Rg (electron density) rg_electron	14.53 Å
Forward intensity I(0) i0	6546230.00
Molecular weight molecular_weight	18169.0 kDa
Excluded volume excluded_volume	22620 Å³
Envelope volume envelope_volume	25145 Å³
Hydration-shell volume shell_volume	14293 Å³
Envelope diameter envelope_diameter	46.4 Å
Shell Rg shell_rg	20.78 Å
Envelope Rg envelope_rg	14.83 Å
Shape Rg shape_rg	14.54 Å
Total Rg total_rg	15.67 Å
Total atoms total_atoms	1273
Residues n_residues	159
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	47.7 Å
Rg (real space) rg_real	15.89 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	6.5460e+06
I(0) uncertainty (real space) i0_real_error	7.2130e+04
Rg (reciprocal space) rg_reciprocal	15.91 Å
I(0) (reciprocal space) i0_reciprocal	6546000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.018
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1634000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.982

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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	DNA helicase
Molecular weight formula_weight	21281.4 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1382

MGSSHHHHHHSSGLVPRGSHMRSTRQIVEFTKAMLQDGADIEPFNRSGEMPLVVKTEGHESLCQKLAQEIGRLKKKGHETIAVICKTAHQCIQAHAHMSEYTDVRLIHKENQPFQKGVCVIPVYLAKGIEFDAVLVYDASEEHYHTEHDRRLLYTACTRAMHMLAVFYTGEASPFVTAVPPHLYQIAE

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6vsxA00
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	106.963 Å
Unit-cell length b length_b	38.813 Å
Unit-cell length c length_c	44.427 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.730 Å
R factor r_factor	0.1752
R_work r_work	0.1723
R_free r_free	0.2015

fit	/app/data/saxs_computation/vs/6vsx/6vsx.fit
pddf	/app/data/pr_computation/vs/6vsx/6vsx.pr.out
profile	/app/data/saxs_computation/vs/6vsx/6vsx.dat

X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD

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

DNA 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

Diffraction experiment Diffraction