PDB-10nh: Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis

ID or keywords:

Entry

Database: PDB / ID: 10nh

Title

Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis

Components

Apurinic endonuclease (APN1)

Keywords

HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Apurinic endonuclease (APN1) / Babesia bovis

Function / homology

Function and homology information

phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function

Biological species

Babesia bovis T2Bo (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis
Authors: Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Jan 28, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10nh.cif.gz	747.4 KB	Display	PDBx/mmCIF format
PDB format	pdb10nh.ent.gz	622.9 KB	Display	PDB format
PDBx/mmJSON format	10nh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0n/10nh ftp://data.pdbj.org/pub/pdb/validation_reports/0n/10nh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Apurinic endonuclease (APN1)

B: Apurinic endonuclease (APN1)

C: Apurinic endonuclease (APN1)

D: Apurinic endonuclease (APN1)

E: Apurinic endonuclease (APN1)

F: Apurinic endonuclease (APN1)

hetero molecules

219 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
Evidence: gel filtration, monomeric
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Apurinic endonuclease (APN1)

hetero molecules

defined by author&software
36.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.625, 93.089, 102.879
Angle α, β, γ (deg.)	91.66, 91.18, 91.09
Int Tables number	1
Space group name H-M	P1

#1: Protein	Apurinic endonuclease (APN1) Mass: 36284.277 Da / Num. of mol.: 6 / Fragment: P53-G367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia bovis T2Bo (eukaryote) / Gene: BBOV_III005900 / Plasmid: BaboA.18322.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S6B9Y3
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-HEZ / HEXANE-1,6-DIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheous D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and ...Details: Morpheous D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM 1,3-Propanediol. BaboA.18322.a.B2.PW39407 at 19.1 mg/mL. 3 Zn ions per subunit. Positive density was observed between the Zn ions which were assigned as imidazole molecules from the crystallant. plate 19997 D1 drop 1, Puck: PSL-2115, Cryo: direct

Crystal

Density Matthews: 2.62 Å³/Da / Density % sol: 53.07 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheous D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 14, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.65→46.52 Å / Num. obs: 62383 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC_1/2: 0.976 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.061 / R_rim(I) all: 0.114 / Χ²: 1.01 / Net I/σ(I): 7.6 / Num. measured all: 218014
Reflection shell	Resolution: 2.65→2.72 Å / % possible obs: 97.7 % / Redundancy: 3.6 % / R_merge(I) obs: 0.706 / Num. measured all: 17068 / Num. unique obs: 4698 / CC_1/2: 0.736 / R_pim(I) all: 0.432 / R_rim(I) all: 0.83 / Χ²: 1.03 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5936: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→46.52 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2635	3210	5.15 %
R_work	0.2052	-	-
obs	0.2083	62274	96.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.65→46.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14736	0	56	155	14947

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	15101
X-RAY DIFFRACTION	f_angle_d	0.635	20364
X-RAY DIFFRACTION	f_dihedral_angle_d	16.463	5555
X-RAY DIFFRACTION	f_chiral_restr	0.042	2242
X-RAY DIFFRACTION	f_plane_restr	0.005	2652

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.65-2.69	0.3539	176	0.2919	2567	X-RAY DIFFRACTION	97
2.69-2.73	0.3416	142	0.2866	2621	X-RAY DIFFRACTION	98
2.73-2.78	0.3469	129	0.2783	2578	X-RAY DIFFRACTION	98
2.78-2.82	0.3801	144	0.2823	2573	X-RAY DIFFRACTION	98
2.82-2.88	0.4272	138	0.3018	2603	X-RAY DIFFRACTION	98
2.88-2.93	0.3788	127	0.2986	2593	X-RAY DIFFRACTION	97
2.93-2.99	0.361	139	0.2731	2565	X-RAY DIFFRACTION	97
2.99-3.06	0.3361	126	0.2601	2582	X-RAY DIFFRACTION	98
3.06-3.13	0.3195	138	0.2428	2645	X-RAY DIFFRACTION	98
3.13-3.2	0.3342	118	0.2425	2525	X-RAY DIFFRACTION	97
3.2-3.29	0.3141	170	0.2395	2517	X-RAY DIFFRACTION	96
3.29-3.39	0.2927	153	0.2427	2563	X-RAY DIFFRACTION	97
3.39-3.5	0.3117	122	0.2354	2600	X-RAY DIFFRACTION	97
3.5-3.62	0.2786	149	0.2038	2534	X-RAY DIFFRACTION	97
3.62-3.77	0.249	151	0.1918	2551	X-RAY DIFFRACTION	97
3.77-3.94	0.2575	155	0.1864	2568	X-RAY DIFFRACTION	97
3.94-4.15	0.2333	150	0.1766	2554	X-RAY DIFFRACTION	97
4.15-4.41	0.2706	113	0.1685	2560	X-RAY DIFFRACTION	96
4.41-4.75	0.1849	112	0.1589	2595	X-RAY DIFFRACTION	97
4.75-5.22	0.2075	172	0.1576	2514	X-RAY DIFFRACTION	96
5.22-5.98	0.2245	90	0.1868	2609	X-RAY DIFFRACTION	96
5.98-7.53	0.2582	125	0.1932	2532	X-RAY DIFFRACTION	96
7.53-46.52	0.2048	171	0.182	2515	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.0575	1.0177	-0.3009	3.1372	-0.3428	2.7372	-0.0808	0.5149	-0.1431	-0.4591	0.004	0.3739	0.0158	-0.5675	0.0878	0.4502	0.0048	-0.0692	0.7183	-0.102	0.5578	-10.4197	-5.4604	-7.8092
2	5.3319	2.8549	-0.9456	3.7893	-0.576	1.3966	-0.0475	0.1147	-0.016	-0.492	-0.0823	-0.1275	-0.1383	-0.1434	0.1321	0.5978	0.103	0.0173	0.5332	-0.0041	0.4844	1.0802	9.7283	-7.4761
3	8.4556	-0.3266	-1.7686	4.0819	0.1675	2.6013	0.3583	-0.1821	0.3351	-0.4327	-0.2132	-0.4487	-0.4586	0.0785	-0.1402	0.5231	-0.0024	0.047	0.4149	0.0049	0.4549	9.1536	13.1903	-0.8759
4	1.7459	0.3636	0.0692	3.9385	0.4443	1.6434	0.1428	-0.0103	-0.2733	-0.008	-0.1631	-0.154	0.0614	-0.0683	-0.0119	0.3232	-0.0041	0.0225	0.4807	0.039	0.4104	3.0593	-3.9955	6.3674
5	3.0564	-1.0939	-0.3866	1.381	-1.0345	2.4498	0.1694	0.2118	-0.8032	-0.2271	0.0663	0.4896	0.5008	-0.541	0.0348	0.5549	-0.1523	0.0661	0.9237	-0.2541	0.858	-11.7149	28.0038	38.0455
6	2.4879	-0.4833	-0.9	1.7334	-0.8885	3.6917	0.1089	0.7095	-0.2721	-0.289	-0.1288	-0.0867	-0.1406	-0.7495	-0.0836	0.5476	-0.0075	0.0573	0.8976	-0.07	0.5702	-7.0196	45.2163	27.4803
7	7.0781	1.5863	-0.9897	1.6986	-0.4186	3.2864	0.1304	0.3745	0.114	-0.0383	-0.0303	-0.5118	-0.6127	-0.1092	-0.0713	0.6584	0.0171	0.121	0.459	-0.0458	0.7262	6.8167	56.6845	33.7127
8	2.5126	-0.6396	0.4637	1.9504	0.0963	2.2178	0.0807	0.0838	-0.1508	-0.0029	-0.0577	-0.2411	0.0711	-0.1182	-0.0201	0.3767	-0.0567	0.1076	0.5808	-0.0856	0.5782	4.9109	41.6582	44.9297
9	2.3348	0.9957	-0.4442	4.5633	-0.2722	3.1539	-0.3392	-0.4965	0.1589	1.4215	0.7836	-0.6156	-0.0663	0.5213	-0.375	0.6796	0.2736	-0.1466	1.1788	0.0291	0.7463	-11.3105	-12.6678	47.7523
10	1.4229	-0.2625	-0.6762	2.4493	0.9566	3.0352	-0.0684	-0.3886	-0.3287	0.3998	0.4365	-0.0778	0.3796	0.0562	-0.2726	0.4551	0.127	0.0155	0.6934	0.0932	0.6009	-18.071	-20.5695	29.6483
11	3.9166	-1.3282	0.9545	2.9372	-1.1692	5.0515	0.0541	0.1162	-0.3	-0.3084	0.2622	0.156	0.1432	-0.3322	-0.2394	0.3282	-0.0985	0.0052	0.5334	0.1515	0.5535	-31.2628	-12.1527	19.9559
12	2.6359	0.3054	0.8517	2.119	-0.1796	4.4537	-0.1457	-0.2736	0.2918	0.2173	0.2559	0.0544	-0.6435	-0.029	-0.1283	0.5702	0.0646	0.0838	0.5636	0.1227	0.4808	-26.8401	-1.6364	34.9055
13	3.331	-0.5219	-0.5941	1.9373	0.745	4.0657	-0.2321	-0.2833	-0.5067	0.1	0.1128	-0.2364	0.5563	0.5423	0.0991	0.4373	0.0433	0.0591	0.4858	0.0465	0.6284	-13.5064	28.6092	74.017
14	2.94	-0.3831	1.4254	1.5276	-0.161	4.2243	-0.0903	0.3882	-0.2406	-0.1356	0.0502	0.21	0.2312	-0.0691	0.0263	0.4368	-0.1035	0.12	0.5008	0.0214	0.6644	-29.2712	34.8968	59.4954
15	2.3659	0.7119	1.0457	1.5549	0.0539	4.1547	-0.2014	-0.0821	0.0676	0.2087	0.0492	0.0812	-0.244	0.0713	0.1724	0.4465	0.0431	0.0929	0.3932	0.0629	0.4414	-24.1422	45.0525	74.7819
16	6.9726	1.8774	-1.174	5.9317	0.0591	5.6885	0.0811	0.0878	0.5039	0.4672	-0.1439	0.5164	-0.7628	0.5826	0.0165	0.7089	0.0447	0.0127	0.4594	0.1212	0.4266	-41.9637	4.7751	71.7453
17	1.2258	-0.4324	-0.6365	3.7497	-0.5363	0.7092	0.0272	-0.1462	0.0663	0.0981	-0.0044	-0.3866	-0.0872	0.5554	-0.1022	0.6054	-0.0239	-0.0477	1.0187	0.0746	0.475	-27.0324	-6.6652	69.2536
18	1.3538	0.1265	-0.7844	4.2128	0.6819	0.9351	-0.1743	0.13	-0.3008	-0.1934	0.1227	-0.1188	0.3831	0.3327	0.0215	0.6859	0.1284	-0.0973	0.8404	0.0894	0.4944	-28.7405	-21.9544	68.2479
19	3.0572	-0.8639	-0.9288	4.9439	0.1498	2.6286	0.1048	0.2501	-0.3031	-0.009	-0.2609	0.6567	0.0215	-0.3101	0.1527	0.6066	-0.0542	-0.0054	0.6195	-0.0257	0.4071	-47.4805	-13.6677	70.135
20	4.3192	1.333	0.7632	2.9663	2.2798	4.4842	0.2236	-0.3366	0.7445	-0.258	-0.6358	0.7652	-0.6426	0.3499	0.2041	0.7791	0.2658	0.0848	0.4442	-0.0241	0.8714	14.1766	55.5185	7.4365
21	2.3577	0.3136	0.6558	3.093	1.8678	2.6918	-0.1433	-0.1349	0.1994	0.1342	0.106	-0.445	-0.0658	0.7049	-0.012	0.559	-0.001	0.008	0.5589	0.1149	0.4685	34.3522	49.9073	5.0879
22	4.7376	-2.1389	-0.7588	6.6003	2.1615	2.8042	-0.1848	-0.106	-0.12	0.3328	0.2652	-0.384	0.5579	0.4891	0.1424	0.4825	0.0989	0.0495	0.5953	0.0718	0.554	39.5274	36.4586	4.8773
23	2.3869	0.8678	-0.0238	3.0238	0.9242	1.7356	0.0863	-0.3074	-0.7804	0.3237	-0.2074	-0.8664	0.2881	0.2049	0.0417	0.6088	0.1569	-0.0335	0.566	0.1056	0.5622	38.3075	26.4836	5.6856
24	3.4005	0.5614	0.2787	2.3277	0.239	1.8834	0.0171	-0.2654	-0.1994	0.185	-0.043	-0.0912	0.4375	0.085	0.031	0.5494	0.0632	0.0464	0.4853	0.055	0.3842	23.6127	27.8641	8.2973
25	7.0779	-1.0174	1.235	7.6109	-0.6817	4.0312	-0.0014	0.0485	0.3234	0.1982	0.0998	0.6049	-0.3722	-0.8121	-0.1476	0.4673	0.0069	0.056	0.4753	0.0456	0.418	15.4651	42.3263	4.473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 55 through 140 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 141 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 218 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 219 through 367 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 55 through 82 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 83 through 141 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 142 through 217 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 218 through 367 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 56 through 82 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 83 through 140 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 141 through 218 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 219 through 366 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 55 through 140 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 141 through 239 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 240 through 367 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 56 through 112 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 113 through 162 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 163 through 239 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 240 through 367 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 55 through 82 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 83 through 140 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 141 through 182 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 183 through 218 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 219 through 309 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 310 through 366 )

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