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9yhl

Crystal structure of Chikungunya virus nsP3 macrodomain N24A D31N double mutant (P31 crystal form) in complex with ADP-ribose

Method: X-RAY DIFFRACTION D_max: 94.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhl
deposition_date	2025-09-30
last_revision	2025-11-26
title	Crystal structure of Chikungunya virus nsP3 macrodomain N24A D31N double 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

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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	30.15 Å
rg_electron	29.40 Å
i0	94118900.00
molecular_weight	72675.0 kDa
excluded_volume	89517 Å³
envelope_volume	115100 Å³
shell_volume	33233 Å³
envelope_diameter	100.8 Å
shell_rg	35.93 Å
envelope_rg	28.97 Å
shape_rg	29.40 Å
total_rg	30.01 Å
total_atoms	10062
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

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3. P(r) Analysis (GNOM)

dmax	94.9 Å
rg_real	30.07 Å
rg_real_error	0.62 Å
i0_real	9.4120e+07
i0_real_error	1.6230e+06
rg_reciprocal	30.11 Å
i0_reciprocal	94120000.0000
total_estimate	0.7027
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	43.0 Å
skewness	0.159
kurtosis	-0.567
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	37410000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.996; Smooth: 0.944

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Non-structural protein 3
formula_weight	18591.1 kDa
ec_number	3.1.3.84
mutation	N24A, D31N
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11383

MKHHHHHHAPSYRVKRMDIAKNDEECVVNAAAPRGLPGNGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT

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	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	660

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6. Citations (1)

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length_a	87.649 Å
length_b	87.649 Å
length_c	85.214 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	1.510 Å
resolution_low	43.820 Å
r_factor	0.1355
r_work	0.1327
r_free	0.1851

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

Crystal structure of Chikungunya virus nsP3 macrodomain N24A D31N double mutant (P31 crystal form) in complex with ADP-ribose

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