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9pmp

Influenza PA-N Endonuclease I38T mutant with compound 1 (3-hydroxy-6-(2-methylphenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid)

Method: X-RAY DIFFRACTION D_max: 53.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pmp
deposition_date	2025-07-18
last_revision	2026-01-21
title	Influenza PA-N Endonuclease I38T mutant with compound 1 (3-hydroxy-6-(2-methylphenyl)-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	17.16 Å
rg_electron	15.97 Å
i0	8455100.00
molecular_weight	21143.0 kDa
excluded_volume	26298 Å³
envelope_volume	29440 Å³
shell_volume	15441 Å³
envelope_diameter	54.5 Å
shell_rg	21.94 Å
envelope_rg	16.18 Å
shape_rg	15.97 Å
total_rg	16.98 Å
total_atoms	1489
n_residues	175
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	53.9 Å
rg_real	17.07 Å
rg_real_error	0.32 Å
i0_real	8.4550e+06
i0_real_error	1.0260e+05
rg_reciprocal	17.08 Å
i0_reciprocal	8455000.0000
total_estimate	0.8191
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.6 Å
skewness	0.173
kurtosis	-0.394
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	2157000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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	22412.5 kDa
ec_number	3.1.-.-
mutation	I38T
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1493

MGSGSAMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAATCTHLEVCFMYSDFGSGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGE

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	3-hydroxy-6-(2-methylphenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid
formula_weight	245.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (1)

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length_a	74.809 Å
length_b	74.809 Å
length_c	118.947 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	2.490 Å
resolution_low	37.400 Å
r_factor	0.2267
r_work	0.2222
r_free	0.2659

fit	/app/data/saxs_computation/pm/9pmp/9pmp.fit
pddf	/app/data/pr_computation/pm/9pmp/9pmp.pr.out
profile	/app/data/saxs_computation/pm/9pmp/9pmp.dat

Influenza PA-N Endonuclease I38T mutant with compound 1 (3-hydroxy-6-(2-methylphenyl)-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