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9uzf

Crystal structure of Kasokero virus cap- snatching endonuclease (D719A mutant)

Method: X-RAY DIFFRACTION D_max: 123.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uzf
deposition_date	2025-05-16
title	Crystal structure of Kasokero virus cap- snatching endonuclease (D719A mutant)
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	35.41 Å
rg_electron	35.83 Å
i0	83508200.00
molecular_weight	72865.0 kDa
excluded_volume	91101 Å³
envelope_volume	119570 Å³
shell_volume	31504 Å³
envelope_diameter	129.9 Å
shell_rg	37.31 Å
envelope_rg	35.81 Å
shape_rg	35.85 Å
total_rg	35.89 Å
total_atoms	5137
n_residues	674
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	123.1 Å
rg_real	35.94 Å
rg_real_error	1.23 Å
i0_real	8.3510e+07
i0_real_error	1.4060e+06
rg_reciprocal	35.61 Å
i0_reciprocal	83480000.0000
total_estimate	0.7660
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.8 Å
skewness	0.658
kurtosis	-0.185
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	8072000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.597; Smooth: 0.392

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 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
atom_count	5252

EVKLEESGGGLVRPGGSRKLSCAASGFTFSSYGMQWVRQAPEKGLEWVAYISSGSRTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYYCATGYGGTWFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 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 3 polymer

description	RNA-directed RNA polymerase L
formula_weight	34311.0 kDa
ec_number	2.7.7.48
mutation	D719A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GPLGSKKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYEGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPAYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

Source

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	115

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6. Citations (1)

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length_a	37.120 Å
length_b	81.150 Å
length_c	116.800 Å
angle_alpha	90.00 °
angle_beta	97.65 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.470 Å
resolution_low	29.330 Å
r_factor	0.2029
r_work	0.2001
r_free	0.2570

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

Crystal structure of Kasokero virus cap- snatching endonuclease (D719A mutant)

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)