PDB-9ob9: Crystal structure of nucleoside-diphosphate kinase from Cryptospo...

ID or keywords:

Entry

Database: PDB / ID: 9ob9

Title

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with ADP and CTP

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
Similarity search - Function

Biological species

Cryptosporidium parvum Iowa II (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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 ADP and CTP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 22, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ob9.cif.gz	202.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ob9.ent.gz	161.2 KB	Display	PDB format
PDBx/mmJSON format	9ob9.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/ob/9ob9 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/9ob9	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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.784, 69.784, 315.704
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-381- 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-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.1 Å³/Da / Density % sol: 41.43 %
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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium ...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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Partial ADP and CTP occupancy at same sites. plate Liu-S-177 D2, Puck: PSL-0514, Cryo: direct from soaking solution

Crystal

Density Matthews: 2.1 Å³/Da / Density % sol: 41.43 %

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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium ...

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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: 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: 1.6→47.98 Å / Num. obs: 61450 / % possible obs: 99.7 % / Redundancy: 16.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.025 / R_rim(I) all: 0.105 / Χ²: 0.93 / Net I/σ(I): 18.9 / Num. measured all: 1030537
Reflection shell	Resolution: 1.6→1.64 Å / % possible obs: 97.7 % / Redundancy: 7.3 % / R_merge(I) obs: 0.92 / Num. measured all: 31376 / Num. unique obs: 4320 / CC_1/2: 0.816 / R_pim(I) all: 0.361 / R_rim(I) all: 0.991 / Χ²: 0.66 / Net I/σ(I) obs: 1.7

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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: 1.6→47.98 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1785	3066	5 %
R_work	0.15	-	-
obs	0.1515	61289	99.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→47.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3501	0	171	372	4044

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3833
X-RAY DIFFRACTION	f_angle_d	1.161	5225
X-RAY DIFFRACTION	f_dihedral_angle_d	18.289	1509
X-RAY DIFFRACTION	f_chiral_restr	0.057	566
X-RAY DIFFRACTION	f_plane_restr	0.011	653

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 (%)
1.6-1.62	0.2844	131	0.2536	2537	X-RAY DIFFRACTION	97
1.63-1.65	0.2499	130	0.239	2512	X-RAY DIFFRACTION	98
1.65-1.68	0.2235	115	0.2034	2582	X-RAY DIFFRACTION	99
1.68-1.71	0.2177	141	0.187	2573	X-RAY DIFFRACTION	99
1.71-1.74	0.2314	148	0.1706	2610	X-RAY DIFFRACTION	100
1.74-1.78	0.1927	122	0.1646	2602	X-RAY DIFFRACTION	100
1.78-1.82	0.1989	138	0.1558	2586	X-RAY DIFFRACTION	100
1.82-1.86	0.1802	151	0.1556	2597	X-RAY DIFFRACTION	100
1.86-1.91	0.1845	117	0.1586	2624	X-RAY DIFFRACTION	100
1.91-1.96	0.2004	145	0.1701	2611	X-RAY DIFFRACTION	100
1.96-2.02	0.1943	141	0.1451	2629	X-RAY DIFFRACTION	100
2.02-2.08	0.1773	153	0.1432	2615	X-RAY DIFFRACTION	100
2.08-2.16	0.1598	130	0.1381	2633	X-RAY DIFFRACTION	100
2.16-2.24	0.1955	152	0.136	2646	X-RAY DIFFRACTION	100
2.24-2.34	0.1803	123	0.139	2650	X-RAY DIFFRACTION	100
2.34-2.47	0.187	159	0.1388	2634	X-RAY DIFFRACTION	100
2.47-2.62	0.1668	147	0.1455	2656	X-RAY DIFFRACTION	100
2.62-2.82	0.1699	134	0.1472	2686	X-RAY DIFFRACTION	100
2.82-3.11	0.1727	157	0.1495	2697	X-RAY DIFFRACTION	100
3.11-3.56	0.1634	148	0.1401	2734	X-RAY DIFFRACTION	100
3.56-4.48	0.1478	146	0.1257	2787	X-RAY DIFFRACTION	100
4.48-47.98	0.1826	138	0.1649	3022	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	0.0682	0.0367	0.0808	0.0222	0.0407	0.1609	-0.0199	-0.024	0.0556	-0.0386	-0.0641	0.0076	-0.0696	-0.1362	-0.0806	0.0891	0.0398	-0.0078	0.1413	-0.0103	0.1542	3.2372	37.2027	19.5947
2	0.0416	-0.01	-0.0341	0.0111	-0.0252	0.1517	-0.0527	-0.0034	0.0404	0.0128	-0.0784	0.053	0.0224	-0.1136	-0.03	0.103	0.0217	-0.0112	0.3489	-0.0503	0.2266	-14.4037	34.7662	13.5815
3	0.9609	-0.0638	0.4906	0.0714	-0.0107	0.2579	-0.1835	0.0539	-0.0015	-0.0396	-0.0553	-0.0216	0.1477	-0.033	-0.0521	0.3694	-0.1365	0.0755	0.3914	-0.0266	0.1639	-11.5308	29.6076	4.388
4	0.0022	-0.0032	-0.0007	0.0054	-0.0012	0.0016	-0.1111	0.0384	-0.0001	-0.0982	-0.0116	-0.1239	0.1079	-0.0573	0	0.204	-0.0605	0.0237	0.3566	-0.0539	0.2525	-11.6418	25.9844	13.618
5	0.0581	0.0338	0.0859	0.0663	0.0748	0.1294	0.0033	0.0431	0.0046	-0.0509	-0.0382	0.0329	-0.0138	-0.1039	-0.0408	0.1078	0.0332	-0.0103	0.1518	-0.0035	0.1677	4.3007	31.9569	11.8511
6	0.0379	0.0094	-0.0527	0.0667	-0.0363	0.0896	-0.0548	-0.004	0.0844	-0.1579	-0.1337	0.0737	-0.0707	-0.073	-0.0829	0.1695	0.1008	-0.0696	0.2126	-0.0246	0.2344	-6.6176	43.4075	9.8575
7	0.1214	-0.0147	0.1965	0.0141	-0.0079	0.3081	-0.109	0.065	0.1193	-0.1358	-0.0172	0.0501	-0.2995	-0.0268	-0.0551	0.195	0.0874	-0.0456	0.1279	-0.0132	0.2433	6.5135	51.4934	19.1847
8	0.173	0.0779	0.027	0.0842	-0.0693	0.2582	-0.0561	-0.0268	0.0178	0.0291	0.0409	0.0594	0.3836	0.1226	0.0052	0.1989	0.0879	0.0062	0.1428	0.0076	0.145	18.6668	12.1687	20.9126
9	0.4228	0.067	0.2849	0.009	0.0447	0.1906	-0.0274	0.1745	-0.0917	-0.2329	0.0008	0.057	-0.0699	0.0935	-0.0105	0.4917	0.2211	-0.0465	0.293	-0.0313	0.1655	30.0794	-0.653	9.5144
10	0.0992	0.0871	-0.0106	0.0787	-0.0034	0.0138	0.0016	0.0658	-0.0062	-0.0899	-0.0126	-0.0084	-0.0473	0.0217	-0.02	0.3765	0.1953	0.0524	0.3199	-0.0089	0.2018	35.3769	4.6976	13.6367
11	0.1141	0.0291	-0.0884	0.0821	0.0482	0.1503	-0.0221	0.0709	0.0089	-0.0605	0.038	0.008	0.2485	0.1435	0.0248	0.1751	0.0645	-0.0007	0.1504	0.0042	0.1512	21.5219	14.961	12.4825
12	0.0617	-0.004	0.0305	0.018	-0.0157	0.0291	-0.0472	0.0138	-0.0699	0.0766	0.0278	-0.0549	0.1242	0.0285	-0.0463	0.5717	0.0999	0.0164	0.016	-0.0809	0.2251	17.4583	-0.3659	12.2286
13	0.1089	0.2064	0.0786	0.3986	0.1688	0.0827	0.0371	0.0034	0.0033	0.1258	-0.1855	0.1416	0.3371	-0.2155	-0.0471	0.3029	-0.065	0.0219	0.1621	0.0301	0.1486	4.5481	8.321	22.6563
14	0.0755	-0.0756	-0.0987	0.072	0.0363	0.3236	0.0319	0.027	0.0022	-0.0209	-0.0204	-0.0002	-0.134	0.2844	0.0045	0.1143	-0.0094	0.0126	0.2433	0.0169	0.1545	33.8734	40.5478	16.6663
15	0.0004	-0.0025	0.0001	0.0097	0.0018	0.0005	-0.014	0.0163	-0.0009	-0.0529	-0.0322	0.0072	-0.0222	-0.0678	-0.0146	0.4191	0.1764	0.0307	0.5942	0.1343	0.1237	33.6558	52.4998	0.5162
16	0.0018	0.0004	0.0021	0.0025	-0.005	0.0062	0.1322	0.0963	0.0073	-0.0211	-0.0366	0.0008	-0.0723	-0.105	0	0.325	0.038	0.0404	0.3002	0.0958	0.2191	30.6239	55.3735	9.9666
17	0.0861	-0.098	-0.0611	0.0828	0.0272	0.1564	0.0099	0.0683	-0.0303	-0.0631	-0.0237	0.0294	-0.0746	0.2155	-0.0075	0.1094	0.0073	0.0051	0.2136	0.0213	0.1568	27.5033	38.2402	10.2275
18	0.0976	0.0435	0.0298	0.1206	-0.0015	0.1945	-0.046	0.0425	-0.0359	-0.0548	0.0848	-0.103	0.0373	0.446	0.1052	-0.0343	0.0371	0.0276	0.4083	0.0096	0.1569	43.1043	32.5774	15.1065

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 154 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 155 through 173 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 25 through 65 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 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 73 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 74 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 143 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 144 through 173 )

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