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9yhe

Crystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P31 crystal form)

Method: X-RAY DIFFRACTION D_max: 101.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhe
deposition_date	2025-09-30
last_revision	2025-11-26
title	Crystal structure of Chikungunya virus nsP3 macrodomain D31N mutant (P31 crystal form)
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	30.57 Å
rg_electron	29.75 Å
i0	96572200.00
molecular_weight	74341.0 kDa
excluded_volume	91809 Å³
envelope_volume	119910 Å³
shell_volume	34474 Å³
envelope_diameter	110.4 Å
shell_rg	36.09 Å
envelope_rg	29.33 Å
shape_rg	29.76 Å
total_rg	30.31 Å
total_atoms	10305
n_residues	664
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	101.5 Å
rg_real	30.52 Å
rg_real_error	1.08 Å
i0_real	9.6570e+07
i0_real_error	1.8040e+06
rg_reciprocal	30.54 Å
i0_reciprocal	96570000.0000
total_estimate	0.8119
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	41.0 Å
skewness	0.242
kurtosis	-0.378
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	23870000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Non-structural protein 3
formula_weight	18634.1 kDa
ec_number	3.1.3.84
mutation	D31N
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11213

MKHHHHHHAPSYRVKRMDIAKNDEECVVNAANPRGLPGNGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT

Source

organism	Chikungunya virus
ncbi_taxonomy_id	37124
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	11

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	649

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6. Citations (1)

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length_a	87.319 Å
length_b	87.319 Å
length_c	85.128 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	1.350 Å
resolution_low	38.850 Å
r_factor	0.1357
r_work	0.1340
r_free	0.1655

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