Klebsiella pneumoniae NagA

Method: X-RAY DIFFRACTION D_max: 187.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9up6
deposition_date	2025-04-27
last_revision	2026-03-04
title	Klebsiella pneumoniae NagA
keywords	Deacetylase, Hydrolase, Carbohydrate metabolism, N-acetylglucosamine-6-phosphate catabolism; HYDROLASE
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	55.19 Å
rg_electron	55.28 Å
i0	1551940000.00
molecular_weight	329330.0 kDa
excluded_volume	411950 Å³
envelope_volume	566760 Å³
shell_volume	85189 Å³
envelope_diameter	188.2 Å
shell_rg	58.14 Å
envelope_rg	54.12 Å
shape_rg	55.28 Å
total_rg	55.33 Å
total_atoms	23076
n_residues	3040
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	187.1 Å
rg_real	55.46 Å
rg_real_error	1.96 Å
i0_real	1.5520e+09
i0_real_error	3.3560e+07
rg_reciprocal	54.94 Å
i0_reciprocal	1551000000.0000
total_estimate	0.8225
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.5 Å
skewness	0.414
kurtosis	-0.596
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	154900000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.573

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	73.520 Å
length_b	73.700 Å
length_c	157.070 Å
angle_alpha	83.70 °
angle_beta	88.96 °
angle_gamma	82.69 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.670 Å
resolution_low	29.440 Å
r_factor	0.2232
r_work	0.2208
r_free	0.2678

description	N-acetylglucosamine-6-phosphate deacetylase
formula_weight	41463.4 kDa
ec_number	3.5.1.25
src_method	man
entity_count	8

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	23076

Klebsiella pneumoniae NagA

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)

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli BL21(DE3)

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

fit	/app/data/saxs_computation/up/9up6/9up6.fit
pddf	/app/data/pr_computation/up/9up6/9up6.pr.out
profile	/app/data/saxs_computation/up/9up6/9up6.dat