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9uzb

Crystal structure of Kasokero virus cap-snatching endonuclease in apo form

Method: X-RAY DIFFRACTION D_max: 123.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uzb
deposition_date	2025-05-16
title	Crystal structure of Kasokero virus cap-snatching endonuclease in apo form
keywords	cap-snatching endonuclease, HYDROLASE; 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	35.77 Å
rg_electron	36.33 Å
i0	86875700.00
molecular_weight	74430.0 kDa
excluded_volume	93077 Å³
envelope_volume	123010 Å³
shell_volume	31877 Å³
envelope_diameter	131.4 Å
shell_rg	37.67 Å
envelope_rg	36.36 Å
shape_rg	36.32 Å
total_rg	36.47 Å
total_atoms	5245
n_residues	677
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	123.3 Å
rg_real	36.32 Å
rg_real_error	1.37 Å
i0_real	8.6880e+07
i0_real_error	1.7000e+06
rg_reciprocal	35.98 Å
i0_reciprocal	86850000.0000
total_estimate	0.7594
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.653
kurtosis	-0.208
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	7308000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.551; Smooth: 0.324

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	33943.6 kDa
ec_number	2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5959

KKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYEGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPDYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

Source

organism	Kasokero virus
ncbi_taxonomy_id	1712570
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	mAb 2E9 Fab heavy chain
formula_weight	24722.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVKLEESGGGLVRPGGSRKLSCAASGFTFSSYGMQWVRQAPEKGLEWVAYISSGSRTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYYCATGYGGTWFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	mAb 2E9 Fab light chain
formula_weight	23971.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QIVLSQSPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	714

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6. Citations (1)

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length_a	37.162 Å
length_b	80.906 Å
length_c	115.184 Å
angle_alpha	90.00 °
angle_beta	93.47 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	27.500 Å
r_factor	0.1842
r_work	0.1823
r_free	0.2207

fit	/app/data/saxs_computation/uz/9uzb/9uzb.fit
pddf	/app/data/pr_computation/uz/9uzb/9uzb.pr.out
profile	/app/data/saxs_computation/uz/9uzb/9uzb.dat

Crystal structure of Kasokero virus cap-snatching endonuclease in apo form

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)