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9pn2

;Influenza PA-N Endonuclease I38T mutant with compound 3 ((6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid) ;

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pn2
deposition_date	2025-07-18
last_revision	2026-01-21
title	;Influenza PA-N Endonuclease I38T mutant with compound 3 ((6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid) ;
keywords	Metal binding protein, endonuclease, influenza endonuclease, LYASE; LYASE
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	17.04 Å
rg_electron	16.03 Å
i0	15807800.00
molecular_weight	19912.0 kDa
excluded_volume	19158 Å³
envelope_volume	30163 Å³
shell_volume	15744 Å³
envelope_diameter	54.6 Å
shell_rg	22.07 Å
envelope_rg	16.24 Å
shape_rg	16.01 Å
total_rg	16.83 Å
total_atoms	1503
n_residues	178
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	54.3 Å
rg_real	16.94 Å
rg_real_error	0.26 Å
i0_real	1.5810e+07
i0_real_error	1.8890e+05
rg_reciprocal	16.96 Å
i0_reciprocal	15810000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.7 Å
skewness	0.194
kurtosis	-0.401
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	4006000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Polymerase acidic protein
formula_weight	22322.4 kDa
ec_number	3.1.-.-
mutation	I38T
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1536

MGSGSAMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAATCTHLEVCFMYSDGGSGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGE

Source

organism	Influenza A virus (A/California/04/2009(H1N1))
ncbi_taxonomy_id	641501
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid
formula_weight	277.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	33

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6. Citations (1)

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length_a	75.112 Å
length_b	75.112 Å
length_c	118.972 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 62 2 2
int_tables_number	180
crystal_system	hexagonal

resolution	2.390 Å
resolution_low	65.050 Å
r_factor	0.2145
r_work	0.2086
r_free	0.2675

fit	/app/data/saxs_computation/pn/9pn2/9pn2.fit
pddf	/app/data/pr_computation/pn/9pn2/9pn2.pr.out
profile	/app/data/saxs_computation/pn/9pn2/9pn2.dat

;Influenza PA-N Endonuclease I38T mutant with compound 3 ((6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid) ;

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