SAXSdb — 9yfy

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1. Structure Basics

entry_id	9yfy
deposition_date	2025-09-27
title	KrkA D193C Kdo adduct
keywords	glycosyltransferase, 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	31.50 Å
rg_electron	31.00 Å
i0	104220000.00
molecular_weight	84311.0 kDa
excluded_volume	106700 Å³
envelope_volume	131850 Å³
shell_volume	36298 Å³
envelope_diameter	106.9 Å
shell_rg	37.05 Å
envelope_rg	31.28 Å
shape_rg	31.00 Å
total_rg	31.54 Å
total_atoms	11781
n_residues	697
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	105.2 Å
rg_real	31.62 Å
rg_real_error	0.75 Å
i0_real	1.0420e+08
i0_real_error	1.6000e+06
rg_reciprocal	31.57 Å
i0_reciprocal	104200000.0000
total_estimate	0.6859
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	31.6 Å
skewness	0.430
kurtosis	-0.397
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	38940000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.961; Smooth: 0.894

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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	12094

MRHIYITSDFLMTSGEEQDNNIRWVYDFISRPIEIATSYDAKCFSTKKWNVLNFDRKHFFALSNIEYVEDKQFYYNERDINSESIKYIKSIIKNDIILVGYELSEQTRKILDKIKVTYIDIWLHPIRYMDDVLFGLKSNNEEINNKLYTFNIPSETYYLYADRLKVQNYRGYRKNKSYLKDNSALFVGQTLNCKAVFHNGKMLNLLDFKNVFEKVVKKYNHVYYSRHPFVKDGDEEIINYLKKFKNVTLNDDPTYHLLASKEIEYVFSISSSVVHEAKYFGKDVEFLYKPVITIGDHKKDYTSVMHEIFYGHFWASILSPLINVNNVPVVSYFSGKDKTRDALSFYWGYRNIDKVELEHHHHHH

Source

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

Entity 2 non-polymer

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

Entity 3 non-polymer

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

Entity 4 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	256

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6. Citations (1)

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length_a	121.150 Å
length_b	121.150 Å
length_c	131.496 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	2.030 Å
resolution_low	40.440 Å
r_factor	0.2239
r_work	0.2224
r_free	0.2510

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

KrkA D193C Kdo adduct

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