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9uzg

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid (DPBA)

Method: X-RAY DIFFRACTION D_max: 124.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uzg
deposition_date	2025-05-16
title	Crystal structure of Kasokero virus cap- snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid (DPBA)
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	35.87 Å
rg_electron	36.52 Å
i0	88279300.00
molecular_weight	75103.0 kDa
excluded_volume	93912 Å³
envelope_volume	122700 Å³
shell_volume	31755 Å³
envelope_diameter	131.2 Å
shell_rg	37.59 Å
envelope_rg	36.44 Å
shape_rg	36.49 Å
total_rg	36.68 Å
total_atoms	5286
n_residues	680
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	124.3 Å
rg_real	36.43 Å
rg_real_error	1.51 Å
i0_real	8.8280e+07
i0_real_error	1.8590e+06
rg_reciprocal	36.08 Å
i0_reciprocal	88250000.0000
total_estimate	0.7535
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.651
kurtosis	-0.217
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	7911000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.325

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	34355.0 kDa
ec_number	2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5643

GPLGSKKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYEGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPDYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

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 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	2-4-DIOXO-4-PHENYLBUTANOIC ACID
formula_weight	192.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	357

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6. Citations (1)

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length_a	37.224 Å
length_b	80.027 Å
length_c	115.771 Å
angle_alpha	90.00 °
angle_beta	93.19 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.150 Å
resolution_low	28.900 Å
r_factor	0.1837
r_work	0.1812
r_free	0.2326

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

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid (DPBA)

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)