← Back to search

9yhh

Crystal structure of Chikungunya virus nsP3 macrodomain N24A mutant (P31 crystal form) in complex with ADP-ribose

Method: X-RAY DIFFRACTION D_max: 95.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yhh
deposition_date	2025-09-30
last_revision	2025-11-26
title	Crystal structure of Chikungunya virus nsP3 macrodomain N24A mutant (P31 crystal form) in complex with ADP-ribose
keywords	Chikungunya virus, ADP-ribose, AViDD, Advanced Light Source 8.3.1, VIRAL PROTEIN, HYDROLASE; VIRAL PROTEIN,HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.15 Å
rg_electron	29.40 Å
i0	93893000.00
molecular_weight	72762.0 kDa
excluded_volume	89674 Å³
envelope_volume	114870 Å³
shell_volume	33168 Å³
envelope_diameter	100.9 Å
shell_rg	35.98 Å
envelope_rg	28.99 Å
shape_rg	29.40 Å
total_rg	30.01 Å
total_atoms	10075
n_residues	643
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	95.3 Å
rg_real	30.07 Å
rg_real_error	0.63 Å
i0_real	9.3890e+07
i0_real_error	1.4590e+06
rg_reciprocal	30.11 Å
i0_reciprocal	93900000.0000
total_estimate	0.9020
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	43.2 Å
skewness	0.155
kurtosis	-0.575
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	37500000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.955

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Non-structural protein 3
formula_weight	18592.1 kDa
ec_number	3.1.3.84
mutation	N24A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10990

MKHHHHHHAPSYRVKRMDIAKNDEECVVNAAAPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT

Source

organism	Chikungunya virus
ncbi_taxonomy_id	37124
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5-DIPHOSPHORIBOSE
formula_weight	559.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
formula_weight	559.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	615

▶

6. Citations (1)

▶

length_a	87.603 Å
length_b	87.603 Å
length_c	85.360 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 31
int_tables_number	144
crystal_system	—

resolution	1.370 Å
resolution_low	43.800 Å
r_factor	0.1494
r_work	0.1472
r_free	0.1883

fit	/app/data/saxs_computation/yh/9yhh/9yhh.fit
pddf	/app/data/pr_computation/yh/9yhh/9yhh.pr.out
profile	/app/data/saxs_computation/yh/9yhh/9yhh.dat