11kk

Crystal structure of HerA Like Helicae YjgR with NTPase fold from Escherchia coli

Method: X-RAY DIFFRACTION Dmax: 154.1 Å Quality: GOOD

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

HerA like helicase YjgR

Escherichia coli str. K-12 substr. MG1655

UniProt P39342

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 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 1–500 Non-standard monomer:Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;289 K;0.15 M D/L-Malic acid pH 7.0, 20 % (w/v) PEG 3350 Resolution 2.90 Å R-free 0.256

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 YJGR_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–503; UniProt 1–500 Author chain B; PDBConstruct 4–503; UniProt 1–500 Author chain C; PDBConstruct 4–503; UniProt 1–500 Author chain D; PDBConstruct 4–503; UniProt 1–500 Author chain E; PDBConstruct 4–503; UniProt 1–500 Author chain F; PDBConstruct 4–503; UniProt 1–500

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 11kk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11kk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11kk
Deposition date deposition_date2026-03-01
最后修订 last_revision2026-05-06
Structure title titleCrystal structure of HerA Like Helicae YjgR with NTPase fold from Escherchia coli
Keywords keywordsHerA like helicase, NTPase fold, CSBID, Structural Genomics, Center for Structural Biology of Infectious Diseases, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier47.06
Radius of gyration Rg (electron density) rg_electron46.50
Forward intensity I(0) i01506750000.00
Molecular weight molecular_weight318710.0 kDa
Excluded volume excluded_volume396610 ų
Envelope volume envelope_volume529220 ų
Hydration-shell volume shell_volume92303 ų
Envelope diameter envelope_diameter161.3
Shell Rg shell_rg52.68
Envelope Rg envelope_rg45.89
Shape Rg shape_rg46.50
Total Rg total_rg46.71
Total atoms total_atoms22183
Residues n_residues2803
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax154.1
Rg (real space) rg_real46.94
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real1.5070e+09
I(0) uncertainty (real space) i0_real_error2.7920e+07
Rg (reciprocal space) rg_reciprocal47.06
I(0) (reciprocal space) i0_reciprocal1507000000.0000
Solution quality estimate total_estimate0.8658
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.0
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.291
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha134100000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.669

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (2)

9. Files and Curves (10)