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9yfx

KrKA retaining Kdo transferase CMP complex

Method: X-RAY DIFFRACTION D_max: 110.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yfx
deposition_date	2025-09-27
title	KrKA retaining Kdo transferase CMP 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	34.64 Å
rg_electron	34.05 Å
i0	223655000.00
molecular_weight	125820.0 kDa
excluded_volume	159310 Å³
envelope_volume	196370 Å³
shell_volume	47029 Å³
envelope_diameter	112.3 Å
shell_rg	41.41 Å
envelope_rg	33.98 Å
shape_rg	34.01 Å
total_rg	34.73 Å
total_atoms	17610
n_residues	1049
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	110.1 Å
rg_real	34.54 Å
rg_real_error	0.69 Å
i0_real	2.2370e+08
i0_real_error	3.3720e+06
rg_reciprocal	34.61 Å
i0_reciprocal	223700000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	43.1 Å
skewness	0.194
kurtosis	-0.548
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	60160000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.901

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	KrKA
formula_weight	43544.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	17673

MRHIYITSDFLMTSGEEQDNNIRWVYDFISRPIEIATSYDAKCFSTKKWNVLNFDRKHFFALSNIEYVEDKQFYYNERDINSESIKYIKSIIKNDIILVGYELSEQTRKILDKIKVTYIDIWLHPIRYMDDVLFGLKSNNEEINNKLYTFNIPSETYYLYADRLKVQNYRGYRKNKSYLKDNSALFVGQTLNDKAVFHNGKMLNLLDFKNVFEKVVKKYNHVYYSRHPFVKDGDEEIINYLKKFKNVTLNDDPTYHLLASKEIEYVFSISSSVVHEAKYFGKDVEFLYKPVITIGDHKKDYTSVMHEIFYGHFWASILSPLINVNNVPVVSYFSGKDKTRDALSFYWGYRNIDKVELEHHHHHH

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	3

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	63

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6. Citations (1)

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length_a	132.850 Å
length_b	132.850 Å
length_c	197.260 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	2.700 Å
resolution_low	46.970 Å
r_factor	0.2088
r_work	0.2079
r_free	0.2291

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

KrKA retaining Kdo transferase CMP 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