PDB-9yn9: Crystal structure of nucleoside-diphosphate kinase Cryptosporidiu...

ID or keywords:

Entry

Database: PDB / ID: 9yn9

Title

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (GMP complex)

Components

nucleoside-diphosphate kinase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / nucleoside-diphosphate kinase

Function / homology

Function and homology information

nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Cryptosporidium parvum Iowa II (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / 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 nucleoside-diphosphate kinase Cryptosporidium parvum (GMP complex)
Authors: Enayati, P. / Lovell, S. / Liu, L. / Battaile, K.P.

History

Deposition	Oct 10, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yn9.cif.gz	201.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9yn9.ent.gz	160.5 KB	Display	PDB format
PDBx/mmJSON format	9yn9.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/yn/9yn9 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/9yn9	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	#104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

Deposited unit

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

54 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

defined by author&software
Evidence: gel filtration
108 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.766, 69.766, 314.954
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-364- HOH
2	1	B-388- HOH

#1: Protein	nucleoside-diphosphate kinase Mass: 17612.361 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote) Gene: cgd4_1940 / Plasmid: CrpaA.01302.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CR64, nucleoside-diphosphate kinase
#2: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.09 Å³/Da / Density % sol: 41.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Index C6: 1.5 M ammonium sulfate, 100 mM Bis-Tris pH 6.5, 100mM NaCl, CrpaA.01302.a.B2.PW39348 at 9.2 mg/mL. overnight soak in 2mM GMP in crystallant, Liu-S-177 H4 , Puck: PSL-0103, Cryo: 2.5M ammonium sulfate.

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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: Jul 26, 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: 1.64→47.93 Å / Num. obs: 57213 / % possible obs: 100 % / Redundancy: 30.6 % / CC_1/2: 1 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.015 / R_rim(I) all: 0.085 / Χ²: 1 / Net I/σ(I): 24.5 / Num. measured all: 1749540
Reflection shell	Resolution: 1.64→1.67 Å / % possible obs: 100 % / Redundancy: 14.4 % / R_merge(I) obs: 1.611 / Num. measured all: 40003 / Num. unique obs: 2778 / CC_1/2: 0.715 / R_pim(I) all: 0.429 / R_rim(I) all: 1.67 / Χ²: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5833: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.64→47.93 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1757	2839	4.98 %
R_work	0.1477	-	-
obs	0.1491	57047	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.64→47.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3516	0	74	381	3971

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3699
X-RAY DIFFRACTION	f_angle_d	1.039	5005
X-RAY DIFFRACTION	f_dihedral_angle_d	17.19	1480
X-RAY DIFFRACTION	f_chiral_restr	0.058	541
X-RAY DIFFRACTION	f_plane_restr	0.011	638

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 (%)
1.64-1.67	0.311	160	0.2772	2636	X-RAY DIFFRACTION	100
1.67-1.7	0.2701	139	0.251	2649	X-RAY DIFFRACTION	100
1.7-1.73	0.2526	127	0.2211	2638	X-RAY DIFFRACTION	100
1.73-1.77	0.2503	149	0.2076	2643	X-RAY DIFFRACTION	100
1.77-1.81	0.2105	143	0.1824	2648	X-RAY DIFFRACTION	100
1.81-1.85	0.2022	128	0.1607	2676	X-RAY DIFFRACTION	100
1.85-1.89	0.1947	162	0.149	2644	X-RAY DIFFRACTION	100
1.89-1.94	0.1729	128	0.1568	2673	X-RAY DIFFRACTION	100
1.94-2	0.1912	157	0.1533	2641	X-RAY DIFFRACTION	100
2-2.07	0.1946	142	0.1552	2664	X-RAY DIFFRACTION	100
2.07-2.14	0.1495	141	0.135	2675	X-RAY DIFFRACTION	100
2.14-2.23	0.1714	139	0.1351	2700	X-RAY DIFFRACTION	100
2.23-2.33	0.1804	141	0.1329	2730	X-RAY DIFFRACTION	100
2.33-2.45	0.1967	145	0.143	2659	X-RAY DIFFRACTION	100
2.45-2.6	0.1667	135	0.1479	2731	X-RAY DIFFRACTION	100
2.6-2.8	0.1576	130	0.1476	2759	X-RAY DIFFRACTION	100
2.8-3.09	0.1913	139	0.1459	2738	X-RAY DIFFRACTION	100
3.09-3.53	0.1614	132	0.1369	2806	X-RAY DIFFRACTION	100
3.53-4.45	0.1437	150	0.1195	2832	X-RAY DIFFRACTION	100
4.45-47.93	0.1754	152	0.1618	3066	X-RAY DIFFRACTION	100

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	4.2856	-0.3504	0.0669	7.5042	3.1163	6.0143	-0.0536	-0.3501	0.3327	0.3044	-0.0238	0.1212	-0.1688	-0.0573	0.1556	0.2054	-0.0517	-0.0029	0.2527	0.0039	0.2303	-2.5148	43.1867	-12.6752
2	0.8267	-0.9452	-0.1376	1.4118	0.2751	1.0518	0.0049	0.0339	-0.016	-0.0382	-0.0576	0.008	0.0058	-0.0007	0.0399	0.1882	-0.0615	-0.0035	0.2414	0.002	0.2217	-3.9539	35.5073	-21.3633
3	6.9614	-2.0416	-4.1573	2.2013	1.7492	3.6028	0.0232	-0.7562	0.5435	0.0935	0.2048	-0.6568	-0.0265	0.9211	-0.2535	0.2197	-0.0115	-0.0347	0.3869	0.0119	0.3863	14.3081	34.8604	-13.476
4	3.5156	-3.386	-0.5564	7.966	-0.4193	5.6484	-0.2828	-0.8969	-0.4041	0.9061	0.4506	-0.3485	0.2453	-0.259	-0.1025	0.4989	0.0556	-0.0229	0.5749	0.0364	0.3238	12.3234	29.9213	-4.2487
5	7.9002	1.0295	3.4132	6.5707	-2.2562	2.6119	0.0135	-0.6244	-0.8252	0.353	-0.0404	0.272	0.9831	0.0505	0.0591	0.4323	0.0257	-0.0015	0.4068	0.0354	0.3563	11.5709	25.824	-13.4645
6	1.7955	-0.6092	-0.4865	1.2676	0.2546	0.4571	0.0022	-0.1156	0.0971	0.1775	-0.0225	-0.0082	-0.0289	0.0198	0.0272	0.2038	-0.0604	-0.017	0.2739	-0.0181	0.2192	-4.5233	39.2419	-13.1062
7	0.614	0.312	0.0413	2.202	-0.4937	0.8405	0.0105	-0.1274	-0.0938	0.0781	0.0927	-0.0952	0.006	0.0601	-0.0808	0.1795	-0.045	-0.0071	0.2513	-0.0021	0.1953	-4.6728	26.7553	-10.8445
8	7.4718	-0.7854	-3.9782	1.4541	-0.6182	5.7632	-0.0818	-0.6372	0.3914	0.4224	0.0096	-0.197	-0.2561	0.4245	-0.0982	0.2717	-0.0699	-0.08	0.2755	-0.0013	0.3307	6.3616	43.3288	-9.8186
9	5.4496	-0.2651	0.2095	1.6398	-0.5378	1.0994	0.0204	-0.0203	0.2813	0.0618	-0.0565	-0.0521	-0.1258	-0.0024	0.02	0.2343	-0.0646	-0.0096	0.2135	-0.0422	0.27	-7.1205	51.5174	-19.0744
10	7.5748	4.5531	-2.5101	8.4515	-4.516	6.8484	-0.1908	-0.1311	-0.4114	-0.1086	0.0782	-0.0778	0.2895	-0.3006	0.0638	0.1599	-0.0384	0.0305	0.3682	-0.0344	0.2523	-38.7397	34.6362	-12.0466
11	0.1852	0.573	-0.167	2.2152	-0.2977	0.6531	0.0143	0.0091	0.0211	0.0118	-0.0159	0.0321	-0.0115	-0.1215	0.0052	0.1685	-0.036	0.0163	0.2872	-0.0111	0.2227	-31.1708	38.2067	-20.0538
12	9.8339	1.8961	-0.9734	5.0336	-4.7481	4.5526	0.3285	0.1256	0.3581	0.5387	0.0838	1.1546	-0.8914	-0.6605	-0.3806	0.371	0.0316	0.0596	0.3451	-0.0452	0.3966	-39.7341	53.2321	-10.3989
13	4.9426	1.5417	2.8312	6.2338	3.7374	6.5983	0.2402	-0.7491	0.2927	0.3493	0.0124	-0.1454	-0.289	0.8606	-0.2831	0.3336	-0.0468	0.033	0.4232	-0.1094	0.3226	-32.6512	54.2416	-5.3995
14	0.7698	-0.1056	-0.0619	3.2825	-2.246	1.894	-0.0827	-0.1214	-0.0314	0.1597	0.0391	-0.0571	0.0115	-0.1667	0.0254	0.2061	-0.0297	0.0238	0.3355	-0.025	0.2392	-34.2066	34.5971	-12.0674
15	4.1976	1.3555	-0.4322	1.9107	-0.9498	1.5476	0.1341	-0.2629	0.0012	0.1401	-0.0445	-0.04	-0.0512	-0.0873	-0.0793	0.179	-0.0322	0.004	0.2708	-0.0335	0.174	-23.3334	40.7585	-9.0458
16	2.34	-3.4687	3.308	5.195	-4.9719	4.8887	-0.0115	-0.4662	0.1553	0.2862	0.3412	0.5264	-0.1493	-0.5371	-0.3483	0.1674	-0.0204	0.028	0.3527	-0.031	0.245	-43.0401	41.7864	-7.7033
17	2.5701	-1.6315	0.2564	3.2038	1.0572	0.9423	0.0322	0.0491	-0.1018	-0.129	-0.0667	0.2588	-0.0061	-0.1228	0.0267	0.1936	-0.0923	0.0405	0.3906	0.018	0.3002	-43.5574	27.5764	-19.2088
18	8.4253	-5.7371	4.7566	5.1859	-2.6604	3.0098	0.1094	0.3944	0.2031	-0.139	-0.1394	-0.3016	0.3909	0.0919	0.0653	0.2611	-0.0758	0.045	0.2694	0.0109	0.2133	-13.2582	7.6258	-15.0731
19	2.5132	0.2289	0.6812	0.1188	-0.2245	0.8755	-0.0501	-0.0165	0.0377	-0.0317	0.0331	0.1036	0.0701	-0.1126	0.0212	0.2357	-0.0756	0.0117	0.2587	-0.0129	0.2258	-20.2669	13.367	-22.3399
20	3.9617	3.7608	5.9191	8.8533	5.5913	8.908	0.5614	-0.4404	-0.4788	0.6663	-0.1277	-0.1694	0.5351	-0.4236	-0.4032	0.3589	-0.1271	0.0029	0.3376	0.0488	0.3114	-29.3349	-2.446	-14.4529
21	3.7363	-2.9872	-2.9794	5.7932	0.7657	3.1761	0.503	-1.067	-0.1258	0.6973	0.0656	0.3909	-0.5256	-0.5587	-0.5658	0.6436	-0.0769	-0.007	0.5708	0.0415	0.3653	-31.6042	1.1819	-4.8301
22	9.6398	2.8359	-4.9579	2.355	-2.2601	2.9732	0.0838	-0.5613	0.5878	0.8533	-0.0782	0.6729	-0.1632	-0.6225	0.0279	0.4924	-0.1073	0.1032	0.4834	-0.0241	0.4221	-35.6748	4.4679	-13.6219
23	2.9908	0.9127	1.5366	0.9928	0.9529	2.05	0.047	-0.0461	-0.1204	0.0756	0.0563	-0.0491	0.2038	-0.0514	-0.0888	0.225	-0.0642	-0.0056	0.2237	0.0122	0.2136	-15.8653	11.3869	-14.736
24	3.9357	-1.3387	0.6073	2.2246	-0.3045	1.0417	0.0349	-0.2727	0.0131	0.1379	0.0295	0.1348	0.1286	-0.1573	-0.0675	0.258	-0.086	0.024	0.2904	0.0099	0.2163	-26.1055	17.5227	-10.6239
25	9.0765	5.9446	0.7201	7.4256	3.8588	7.3277	0.2379	-0.3652	-0.6391	0.2625	-0.1855	-0.3336	0.8867	0.0532	-0.0882	0.358	-0.0582	0.008	0.2315	0.0627	0.3149	-17.7104	-0.4751	-11.7929
26	6.6783	2.8313	-2.1785	5.911	-1.3453	3.8998	-0.1572	0.1967	-0.6379	-0.2519	0.0484	-0.5114	0.3837	0.0027	0.0469	0.2651	0.0335	-0.0128	0.2497	0.0166	0.2418	-4.8573	8.0578	-22.4178

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 75 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 76 through 84 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 85 through 105 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 106 through 136 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 137 through 147 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 148 through 166 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 18 through 26 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 27 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 66 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 67 through 85 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 86 through 105 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 106 through 136 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 137 through 147 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 148 through 166 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 18 through 26 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 27 through 58 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 59 through 66 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 67 through 75 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 76 through 84 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 85 through 105 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 106 through 136 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 137 through 147 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 148 through 166 )

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