SAXSdb — 9umd

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1. Structure Basics

entry_id	9umd
deposition_date	2025-04-21
last_revision	2026-04-29
title	autoinhibited kpNLRL
keywords	bacterial immune system, NLR-like, IMMUNE SYSTEM; IMMUNE SYSTEM
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	57.11 Å
rg_electron	57.17 Å
i0	2039380000.00
molecular_weight	385760.0 kDa
excluded_volume	486280 Å³
envelope_volume	702520 Å³
shell_volume	104010 Å³
envelope_diameter	210.4 Å
shell_rg	57.79 Å
envelope_rg	56.19 Å
shape_rg	57.14 Å
total_rg	57.30 Å
total_atoms	27148
n_residues	3296
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	198.5 Å
rg_real	57.26 Å
rg_real_error	2.57 Å
i0_real	2.0390e+09
i0_real_error	4.6870e+07
rg_reciprocal	56.97 Å
i0_reciprocal	2038000000.0000
total_estimate	0.8633
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.8 Å
skewness	0.435
kurtosis	-0.173
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	193100000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.765

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Tetratricopeptide repeat protein
formula_weight	96073.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	27148

MIKAFLSHSSKDKEHYVRNVANWLGKENIIYDEFTFEEGERTLDQIMEGLGDSELFVLFISNSALESEWVKKEITESKKLLDEGKILKIFPIIIDNNINHEDQRIPDWLRKDYNLQPITRARTAASRIKNHLYKISWQKHPKLEKISSLFVGRNDKLEEFEERINDYTKKKPTVIFASGLIGVGRRSFLSKALIKCNIQKNQITPYAIYLDRNESIEDFILKLNDLGITDLKESALSLSEKTIEEKQKIISNILNEAYKAKETIFFLDDGCIINYKRELTPWFKMIIEEYNDINFPVLCIASRYRVNFANRPRDDRFYFIELPELNVKERRRLLSQLLEIENIDDLDPSNFSSVCDLLTGLPEQVRFAIELIKDKNIIPFENKLPILSDFNNDKASIQLQRYAHNETVLDFIRLIAQFEVITLDFIFSIVDKDKYLPVLEALIAESICELVGSDGEMIRLNDIVRDYIKRNRLKINDEHNKKLNLVVKEIVNNEDLTEANSSVYIFTIKEMLKSDEYIDPKHLIPSHYLRCMKDLYNAKGSLEKVISLADTILQKEKNMDNGVVQDIRYYLCLALAKKSDSRLLTEVQKIRGDEHKFLLGFYYRKCGRLSDALSQFESIINAPYVESRAKRELVQVYTQLEEYDKALSYAKKNYEENRSNQFHCQAYFNCLINSQHRVDSDNIVLKDIITTLINIDSEQSNEMAKIADAMYSAKIENDVVKSITIINDCIATYPESPYPLLAKCDVGLKFKSIQTLEEALSSLDKMKRRKVVSERTLTTYQAYLMALKGDENSANQIISNDIKKYPQEARERILKRIKEYAGKN

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	77.243 Å
length_b	150.856 Å
length_c	381.728 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	4.140 Å
resolution_low	140.300 Å
r_factor	0.2564
r_work	0.2516
r_free	0.3353

fit	/app/data/saxs_computation/um/9umd/9umd.fit
pddf	/app/data/pr_computation/um/9umd/9umd.pr.out
profile	/app/data/saxs_computation/um/9umd/9umd.dat

autoinhibited kpNLRL

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)