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9yhc

Crystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)

Method: X-RAY DIFFRACTION D_max: 102.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhc
deposition_date	2025-09-30
last_revision	2025-11-26
title	Crystal structure of Chikungunya virus nsP3 macrodomain D31H 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	30.72 Å
rg_electron	29.88 Å
i0	93979100.00
molecular_weight	73389.0 kDa
excluded_volume	90653 Å³
envelope_volume	119340 Å³
shell_volume	34042 Å³
envelope_diameter	110.6 Å
shell_rg	36.27 Å
envelope_rg	29.57 Å
shape_rg	29.90 Å
total_rg	30.42 Å
total_atoms	10165
n_residues	657
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	102.0 Å
rg_real	30.67 Å
rg_real_error	0.94 Å
i0_real	9.3980e+07
i0_real_error	1.5910e+06
rg_reciprocal	30.69 Å
i0_reciprocal	93980000.0000
total_estimate	0.8112
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	41.2 Å
skewness	0.241
kurtosis	-0.394
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	26260000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; 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	18658.2 kDa
ec_number	3.1.3.84
mutation	D31H
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11174

MKHHHHHHAPSYRVKRMDIAKNDEECVVNAANPRGLPGHGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT

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	5

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	13

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	633

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6. Citations (1)

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length_a	87.445 Å
length_b	87.445 Å
length_c	85.293 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	38.910 Å
r_factor	0.1375
r_work	0.1356
r_free	0.1718

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