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10nh

Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis

Method: X-RAY DIFFRACTION D_max: 154.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10nh
deposition_date	2026-01-28
last_revision	2026-02-11
title	Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Apurinic endonuclease (APN1), Babesia bovis, HYDROLASE ;; 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	46.77 Å
rg_electron	46.39 Å
i0	660893000.00
molecular_weight	211220.0 kDa
excluded_volume	263430 Å³
envelope_volume	369100 Å³
shell_volume	66179 Å³
envelope_diameter	157.8 Å
shell_rg	51.62 Å
envelope_rg	44.51 Å
shape_rg	46.38 Å
total_rg	46.62 Å
total_atoms	14792
n_residues	1874
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	154.5 Å
rg_real	46.66 Å
rg_real_error	1.57 Å
i0_real	6.6090e+08
i0_real_error	1.1930e+07
rg_reciprocal	46.77 Å
i0_reciprocal	661000000.0000
total_estimate	0.8955
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.1 Å
skewness	0.155
kurtosis	-0.597
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	31350000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Apurinic endonuclease (APN1)
formula_weight	36284.3 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	14947

MAHHHHHHPKPWVTLPKLDPNEDRDAAFAEIAAASAASGLYIGAHISTAGGLDNSVINAYNICGQAFALFLKNQRRWDSPPLADATVKKFTANIEKYKYDIRYVLPHGSYLINIANPDYEKRMKSYHHFVDDIQRCEKLGITLYNFHPGSTVGMCEKPEGIRNIANCINMAMKETSSAKIVLENAAGQKNVIGSTFEDLRDIINLVENKDRVAVCLDTCHLFAAGYDIRTKDKFEAVMRSFDEIIGLKYLVAVHLNDCKSDLGSGLDRHENIGIGKLTRETFEFIANSGYFRNMPIILETPDIHGDETIYKQEVKVMYGLVEG

Source

organism	Babesia bovis T2Bo
ncbi_taxonomy_id	484906
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	18

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	HEXANE-1,6-DIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	155

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6. Citations (1)

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length_a	59.625 Å
length_b	93.089 Å
length_c	102.879 Å
angle_alpha	91.66 °
angle_beta	91.18 °
angle_gamma	91.09 °
z_pdb	6

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.650 Å
resolution_low	46.520 Å
r_factor	0.2083
r_work	0.2052
r_free	0.2635

fit	/app/data/saxs_computation/0n/10nh/10nh.fit
pddf	/app/data/pr_computation/0n/10nh/10nh.pr.out
profile	/app/data/saxs_computation/0n/10nh/10nh.dat