← Back to search

9uzd

Crystal structure of Kasokero virus cap- snatching endonuclease (E668A mutant)

Method: X-RAY DIFFRACTION D_max: 123.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uzd
deposition_date	2025-05-16
title	Crystal structure of Kasokero virus cap- snatching endonuclease (E668A mutant)
keywords	cap-snatching endonuclease, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.39 Å
rg_electron	35.73 Å
i0	83194900.00
molecular_weight	72423.0 kDa
excluded_volume	90413 Å³
envelope_volume	118990 Å³
shell_volume	31374 Å³
envelope_diameter	130.4 Å
shell_rg	37.26 Å
envelope_rg	35.81 Å
shape_rg	35.73 Å
total_rg	35.82 Å
total_atoms	5103
n_residues	675
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

▼

3. P(r) Analysis (GNOM)

dmax	123.5 Å
rg_real	35.93 Å
rg_real_error	1.78 Å
i0_real	8.3190e+07
i0_real_error	1.5750e+06
rg_reciprocal	35.60 Å
i0_reciprocal	83170000.0000
total_estimate	0.7646
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.2 Å
skewness	0.665
kurtosis	-0.173
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	7794000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.580; Smooth: 0.467

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	34297.0 kDa
ec_number	2.7.7.48
mutation	E668A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5239

GPLGSKKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYAGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPDYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

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	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	136

▶

6. Citations (1)

▶

length_a	37.189 Å
length_b	80.332 Å
length_c	116.262 Å
angle_alpha	90.00 °
angle_beta	97.74 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	29.300 Å
r_factor	0.1932
r_work	0.1905
r_free	0.2475

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

Crystal structure of Kasokero virus cap- snatching endonuclease (E668A 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)