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11kk

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

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11kk
deposition_date	2026-03-01
last_revision	2026-05-06
title	Crystal structure of HerA Like Helicae YjgR with NTPase fold from Escherchia coli
keywords	HerA like helicase, NTPase fold, CSBID, Structural Genomics, Center for Structural Biology of Infectious Diseases, GENE REGULATION; GENE REGULATION
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	47.06 Å
rg_electron	46.50 Å
i0	1506750000.00
molecular_weight	318710.0 kDa
excluded_volume	396610 Å³
envelope_volume	529220 Å³
shell_volume	92303 Å³
envelope_diameter	161.3 Å
shell_rg	52.68 Å
envelope_rg	45.89 Å
shape_rg	46.50 Å
total_rg	46.71 Å
total_atoms	22183
n_residues	2803
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	154.1 Å
rg_real	46.94 Å
rg_real_error	1.08 Å
i0_real	1.5070e+09
i0_real_error	2.7920e+07
rg_reciprocal	47.06 Å
i0_reciprocal	1507000000.0000
total_estimate	0.8658
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.0 Å
skewness	0.294
kurtosis	-0.291
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0001
highest_alpha	134100000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.669

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HerA like helicase YjgR
formula_weight	55274.0 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	22184

SNAMSEPLLIARTPDTELFLLPGMANRHGLITGATGTGKTVTLQKLAESLSEIGVPVFMADVKGDLTGVAQAGTVSEKLLARLKNIGVNDWQPHANPVVVWDIFGEKGHPVRATVSDLGPLLLARLLNLNDVQSGVLNIIFRIADDQGLLLLDFKDLRAITQYIGDNAKSFQNQYGNISSASVGAIQRGLLSLEQQGAAHFFGEPMLDIKDWMRTDANGKGVINILSAEKLYQMPKLYAASLLWMLSELYEQLPEAGDLEKPKLVFFFDEAHLLFNDAPQVLLDKIEQVIRLIRSKGVGVWFVSQNPSDIPDNVLGQLGNRVQHALRAFTPKDQKAVKAAAQTMRANPAFDTEKAIQELGTGEALISFLDAKGSPSVVERAMVIAPCSRMGPVTEDERNGLINHSPVYGKYEDEVDRESAYEMLQKGFQASTEQQNNPPAKGKEVAVDDGILGGLKDILFGTTGPRGGKKDGVVQTMAKSAARQVTNQIVRGMLGSLLGGRRR

Source

organism	Escherichia coli str. K-12 substr. MG1655
ncbi_taxonomy_id	511145
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (2)

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length_a	77.645 Å
length_b	229.362 Å
length_c	99.531 Å
angle_alpha	90.00 °
angle_beta	112.88 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.900 Å
resolution_low	47.040 Å
r_factor	0.2180
r_work	0.2160
r_free	0.2560

fit	/app/data/saxs_computation/1k/11kk/11kk.fit
pddf	/app/data/pr_computation/1k/11kk/11kk.pr.out
profile	/app/data/saxs_computation/1k/11kk/11kk.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction