SAXSdb — 9yfz

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1. Structure Basics

entry_id	9yfz
deposition_date	2025-09-27
title	KrkA D193C ternary complex
keywords	glycosyltransferase; capsule biosynthesis, TRANSFERASE; TRANSFERASE
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	31.65 Å
rg_electron	31.09 Å
i0	103098000.00
molecular_weight	84021.0 kDa
excluded_volume	106370 Å³
envelope_volume	131490 Å³
shell_volume	36253 Å³
envelope_diameter	107.2 Å
shell_rg	37.01 Å
envelope_rg	31.24 Å
shape_rg	31.06 Å
total_rg	31.72 Å
total_atoms	11724
n_residues	691
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	106.1 Å
rg_real	31.79 Å
rg_real_error	0.82 Å
i0_real	1.0310e+08
i0_real_error	1.6820e+06
rg_reciprocal	31.74 Å
i0_reciprocal	103100000.0000
total_estimate	0.8754
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.8 Å
skewness	0.439
kurtosis	-0.398
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	45210000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.902

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	KrKA
formula_weight	43532.4 kDa
mutation	D193C
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12086

MRHIYITSDFLMTSGEEQDNNIRWVYDFISRPIEIATSYDAKCFSTKKWNVLNFDRKHFFALSNIEYVEDKQFYYNERDINSESIKYIKSIIKNDIILVGYELSEQTRKILDKIKVTYIDIWLHPIRYMDDVLFGLKSNNEEINNKLYTFNIPSETYYLYADRLKVQNYRGYRKNKSYLKDNSALFVGQTLNCKAVFHNGKMLNLLDFKNVFEKVVKKYNHVYYSRHPFVKDGDEEIINYLKKFKNVTLNDDPTYHLLASKEIEYVFSISSSVVHEAKYFGKDVEFLYKPVITIGDHKKDYTSVMHEIFYGHFWASILSPLINVNNVPVVSYFSGKDKTRDALSFYWGYRNIDKVELEHHHHHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

description	beta-D-ribofuranose-(1-7)-methyl 3-deoxy-beta-D-manno-oct-2-ulopyranosidonic acid
formula_weight	384.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CYTIDINE-5'-MONOPHOSPHATE
formula_weight	323.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
formula_weight	238.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	352

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6. Citations (1)

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length_a	121.719 Å
length_b	121.719 Å
length_c	131.962 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	hexagonal

resolution	2.210 Å
resolution_low	41.180 Å
r_factor	0.2231
r_work	0.2216
r_free	0.2532

fit	/app/data/saxs_computation/yf/9yfz/9yfz.fit
pddf	/app/data/pr_computation/yf/9yfz/9yfz.pr.out
profile	/app/data/saxs_computation/yf/9yfz/9yfz.dat

KrkA D193C ternary complex

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