PDB-9oai: Crystal structure of nucleoside-diphosphate kinase from Cryptospo...

ID or keywords:

Entry

Database: PDB / ID: 9oai

Title

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with thymidine-5'-phosphate

Components

nucleoside-diphosphate kinase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

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: 1.51 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 in complex with thymidine-5'-phosphate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 21, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9oai.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9oai.ent.gz	156.8 KB	Display	PDB format
PDBx/mmJSON format	9oai.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/9oai ftp://data.pdbj.org/pub/pdb/validation_reports/oa/9oai	HTTPS FTP

-
Related structure data

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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.879, 69.879, 316.209
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-394- HOH
2	1	A-433- HOH
3	1	C-359- 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-TMP / THYMIDINE-5'-PHOSPHATE Mass: 322.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, ...Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. plate Liu-S-177 D2, Puck: PSL-0505, Cryo: direct from soaking solution

Crystal

Density Matthews: 2.11 Å³/Da / Density % sol: 41.68 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, ...

-
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: Apr 5, 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: 1.51→48.05 Å / Num. obs: 70384 / % possible obs: 96.3 % / Redundancy: 15.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.023 / R_rim(I) all: 0.096 / Χ²: 0.92 / Net I/σ(I): 20 / Num. measured all: 1085637
Reflection shell	Resolution: 1.51→1.55 Å / % possible obs: 76.5 % / Redundancy: 4.9 % / R_merge(I) obs: 0.737 / Num. measured all: 19240 / Num. unique obs: 3961 / CC_1/2: 0.669 / R_pim(I) all: 0.356 / R_rim(I) all: 0.824 / Χ²: 0.7 / Net I/σ(I) obs: 1.7

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_5438: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.51→48.05 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.163	3475	4.95 %
R_work	0.1421	-	-
obs	0.1432	70227	96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.51→48.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3497	0	67	467	4031

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3721
X-RAY DIFFRACTION	f_angle_d	1.03	5044
X-RAY DIFFRACTION	f_dihedral_angle_d	17.257	1506
X-RAY DIFFRACTION	f_chiral_restr	0.064	550
X-RAY DIFFRACTION	f_plane_restr	0.011	647

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 (%)
1.51-1.53	0.2868	101	0.3048	1936	X-RAY DIFFRACTION	71
1.53-1.55	0.3107	128	0.2686	2159	X-RAY DIFFRACTION	79
1.55-1.58	0.2442	112	0.2256	2261	X-RAY DIFFRACTION	85
1.58-1.6	0.1954	111	0.186	2394	X-RAY DIFFRACTION	87
1.6-1.63	0.1909	120	0.1657	2442	X-RAY DIFFRACTION	89
1.63-1.65	0.1972	128	0.1583	2573	X-RAY DIFFRACTION	94
1.65-1.68	0.182	134	0.1455	2598	X-RAY DIFFRACTION	95
1.68-1.72	0.1774	126	0.1397	2669	X-RAY DIFFRACTION	98
1.72-1.75	0.1875	156	0.1342	2742	X-RAY DIFFRACTION	100
1.75-1.79	0.1614	151	0.1432	2736	X-RAY DIFFRACTION	100
1.79-1.83	0.1692	148	0.1347	2733	X-RAY DIFFRACTION	100
1.83-1.88	0.1657	134	0.1395	2731	X-RAY DIFFRACTION	100
1.88-1.93	0.1675	123	0.145	2771	X-RAY DIFFRACTION	100
1.93-1.99	0.1742	139	0.1396	2771	X-RAY DIFFRACTION	100
1.99-2.05	0.1581	151	0.1247	2755	X-RAY DIFFRACTION	100
2.05-2.12	0.1477	140	0.1211	2772	X-RAY DIFFRACTION	100
2.12-2.21	0.1496	137	0.1253	2775	X-RAY DIFFRACTION	100
2.21-2.31	0.1463	141	0.1243	2769	X-RAY DIFFRACTION	100
2.31-2.43	0.1413	150	0.1284	2800	X-RAY DIFFRACTION	100
2.43-2.58	0.1522	157	0.1367	2788	X-RAY DIFFRACTION	100
2.58-2.78	0.1672	137	0.1388	2831	X-RAY DIFFRACTION	100
2.78-3.06	0.1488	164	0.1468	2824	X-RAY DIFFRACTION	100
3.06-3.5	0.1686	159	0.1389	2865	X-RAY DIFFRACTION	100
3.5-4.41	0.1325	166	0.1233	2913	X-RAY DIFFRACTION	100
4.41-48.05	0.1773	162	0.1597	3144	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	0.4359	0.0661	0.0839	0.2761	0.036	0.2016	-0.0126	0.0094	0.0292	-0.0293	-0.0109	0.0193	0.0002	-0.0045	-0.0056	0.0842	0.0127	0.0058	0.0978	0.004	0.0944	3.5279	37.175	19.6186
2	0.0132	0.0146	-0.0123	0.0188	0.0068	0.028	-0.0415	0.0857	0.0668	-0.0016	-0.0791	0.2112	-0.003	-0.2326	-0.0015	0.0939	0.0019	-0.0042	0.1815	-0.0066	0.1668	-14.302	34.8172	13.6501
3	0.1018	0.1107	-0.0442	0.1248	-0.0346	0.0335	0.0728	0.3726	-0.2278	-0.3226	-0.1736	0.1047	0.5809	-0.2103	-0.0043	0.2146	-0.0039	-0.0291	0.2855	-0.0069	0.1479	-12.3626	29.9222	4.0375
4	0.0104	-0.0017	0.0124	0.0258	0.0015	0.0285	0.1756	0.3247	-0.3546	-0.0292	0.0148	-0.1711	0.5706	0.0641	0	0.2181	0.0026	-0.0281	0.2488	-0.0442	0.1977	-11.496	26.2296	13.3089
5	0.3117	0.052	0.1562	0.5442	0.3988	0.0502	-0.0053	0.0613	-0.0054	-0.0582	0.0311	0.0231	0.0015	-0.0085	0.0088	0.0934	0.0151	0.001	0.1155	0.0087	0.0914	4.6455	32.0536	11.8559
6	0.2539	-0.0513	0.2696	0.3874	-0.0128	0.2178	-0.0101	0.0765	0.1546	-0.1045	-0.0227	0.0828	-0.0469	-0.0224	-0.0095	0.1076	0.023	-0.0074	0.1045	0.0063	0.1317	2.5215	48.6879	15.8571
7	0.4282	-0.0763	-0.0102	0.0627	0.0553	0.2669	-0.0218	-0.0152	-0.0286	-0.0051	0.0137	0.0311	0.0692	0.0148	-0.0156	0.1035	0.0269	0.0029	0.1118	0.0124	0.0972	18.944	12.1272	20.798
8	0.0221	0.0123	0.003	0.0192	-0.0271	0.0355	0.0877	0.008	-0.0441	-0.1779	-0.085	0.0599	-0.0123	-0.0225	-0.0015	0.1911	0.065	-0.0002	0.1373	0.0047	0.1458	29.2213	-2.7973	14.3856
9	0.7005	0.5152	-0.2278	1.2015	-0.0171	0.1271	0.0412	0.3115	0.2212	-0.328	0.1318	0.2338	-0.1988	0.3813	0.0391	0.3312	0.0501	-0.0026	0.2739	-0.0209	0.1004	32.0337	1.1308	4.7915
10	0.0538	-0.0114	-0.0297	0.0049	0.0099	0.0184	0.1011	0.1558	0.41	-0.5016	0.0128	-0.2031	-0.397	0.273	-0.0024	0.274	0.0381	0.0643	0.2198	-0.0034	0.1766	35.6432	4.4166	13.6283
11	0.4919	-0.0406	-0.1608	0.1478	0.0381	0.3571	0.0156	0.0456	-0.0002	-0.0557	0.0055	0.0078	0.0401	0.0239	-0	0.1095	0.0237	-0.0047	0.1061	0.0007	0.0892	21.7672	14.9295	12.2737
12	0.0472	-0.0506	-0.0409	0.0982	0.0532	0.0632	0.094	0.0469	-0.1374	-0.0643	-0.1294	0.1196	0.3948	-0.059	0	0.2115	0.0189	-0.0007	0.1403	-0.0277	0.1888	17.9793	-0.2851	11.6297
13	0.4311	0.2935	-0.3208	0.2167	-0.1053	0.2027	0.0709	0.0973	-0.2371	-0.2042	-0.1148	0.1993	0.1401	-0.0327	-0	0.1418	-0.0004	0.0082	0.1327	0.0009	0.1533	4.5705	8.6347	22.2539
14	0.0694	-0.1557	0.0557	0.3223	0.0067	0.1484	0.0147	0.0158	0.0336	-0.0273	-0.0159	-0.0518	-0.0136	0.0679	-0.0092	0.0801	0.0145	0.01	0.1179	0.0115	0.0969	32.8535	37.6516	18.3682
15	0.2022	-0.0492	-0.0529	0.1398	-0.052	0.0847	0.0313	0.2019	0.0877	0.0038	0.0691	0.0897	-0.0076	-0.0435	0.0008	0.2	-0.0092	0.0233	0.173	0.0419	0.1986	37.2013	53.1283	5.4304
16	0.0051	0.0417	-0.001	0.1034	-0.0511	0.0352	-0.0459	0.2509	0.3026	0.0747	0.2609	0.3671	-0.3058	-0.8007	-0.014	0.1981	0.0345	0.0076	0.2475	0.1014	0.1712	31.081	55.2972	10.0921
17	0.073	0.0641	-0.0207	0.1136	-0.0193	0.1412	-0.0278	0.0404	0.0335	-0.0776	0.003	0.0681	-0.0165	0.0396	-0.0045	0.0957	0.0113	0.0119	0.1362	0.0139	0.1046	34.2269	34.6256	12.1499
18	0.2455	-0.1286	0.1198	0.0728	-0.0126	0.2354	0.0334	0.0781	-0.0106	-0.0595	0.0014	-0.009	-0.0133	0.0438	0.0078	0.0964	0.0034	0.0094	0.1297	0.0136	0.1055	23.3626	40.8212	9.119
19	0.0103	0.0561	-0.0144	0.0692	-0.0319	0.0512	-0.0115	0.1775	0.1471	-0.1479	0.1052	-0.1807	-0.126	0.1754	-0.0001	0.0939	-0.0045	0.0118	0.1536	0.0155	0.1235	43.1256	41.9308	7.7616
20	0.335	-0.153	0.312	0.1647	-0.2968	0.2545	-0.0622	0.0346	-0.1073	-0.1477	0.0214	-0.3127	0.0263	0.0537	-0.0229	0.0881	0.0195	0.019	0.1526	0.0058	0.1227	43.5318	27.4791	19.3092

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 65 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 73 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 74 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 91 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 143 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 144 through 173 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 65 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 66 through 73 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 74 through 82 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 83 through 91 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 92 through 143 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 144 through 154 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 155 through 173 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 25 through 64 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 65 through 82 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 83 through 92 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 93 through 112 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 113 through 143 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 144 through 154 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 155 through 173 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi