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9qpb

;APH(2'')-IVa with an inhibitor ;

Method: X-RAY DIFFRACTION D_max: 111.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpb
deposition_date	2025-03-26
last_revision	2026-02-11
title	;APH(2'')-IVa with an inhibitor ;
keywords	inhibitor, complex, enzyme, ANTIBIOTIC; ANTIBIOTIC
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	32.29 Å
rg_electron	32.40 Å
i0	133308000.00
molecular_weight	62645.0 kDa
excluded_volume	61352 Å³
envelope_volume	110900 Å³
shell_volume	30743 Å³
envelope_diameter	114.9 Å
shell_rg	36.38 Å
envelope_rg	31.94 Å
shape_rg	32.40 Å
total_rg	32.68 Å
total_atoms	4789
n_residues	580
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	111.3 Å
rg_real	32.63 Å
rg_real_error	1.08 Å
i0_real	1.3330e+08
i0_real_error	2.5150e+06
rg_reciprocal	32.49 Å
i0_reciprocal	133300000.0000
total_estimate	0.8229
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.5 Å
skewness	0.516
kurtosis	-0.422
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	11140000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.744; Smooth: 0.791

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	APH(2'')-Id
formula_weight	37596.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	4936

MGSSHHHHHHSSGLVPRGSHMRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK

Source

organism	Enterococcus casseliflavus
ncbi_taxonomy_id	37734
host_organism	Escherichia coli

Entity 2 non-polymer

description	5-bromanyl-1~{H}-pyrrolo[2,3-b]pyridine
formula_weight	197.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	9

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	144

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6. Citations (1)

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length_a	61.632 Å
length_b	63.577 Å
length_c	87.004 Å
angle_alpha	90.00 °
angle_beta	90.25 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.860 Å
resolution_low	44.250 Å
r_factor	0.2131
r_work	0.2110
r_free	0.2521

fit	/app/data/saxs_computation/qp/9qpb/9qpb.fit
pddf	/app/data/pr_computation/qp/9qpb/9qpb.pr.out
profile	/app/data/saxs_computation/qp/9qpb/9qpb.dat

;APH(2'')-IVa with an inhibitor ;

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