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

ID or keywords:

Entry

Database: PDB / ID: 9obc

Title

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

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: 1.62 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 from Cryptosporidium parvum in complex with ADP
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	9obc.cif.gz	199.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9obc.ent.gz	158.6 KB	Display	PDB format
PDBx/mmJSON format	9obc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9obc_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9obc_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9obc_validation.xml.gz	26 KB	Display
Data in CIF	9obc_validation.cif.gz	34.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/9obc ftp://data.pdbj.org/pub/pdb/validation_reports/ob/9obc	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

Deposited unit

A: nucleoside-diphosphate kinase

B: nucleoside-diphosphate kinase

C: nucleoside-diphosphate kinase

hetero molecules

54.2 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)	69.781, 69.781, 315.843
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-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
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 370 / 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: 41.45 %
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, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0. ...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, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. plate Liu-S-177 D2, Puck: PSL-0511, Cryo: direct from soaking solution

Crystal

Density Matthews: 2.1 Å³/Da / Density % sol: 41.45 %

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, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0. ...

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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: 1.62→47.99 Å / Num. obs: 58837 / % possible obs: 99.1 % / Redundancy: 17.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.024 / R_rim(I) all: 0.101 / Χ²: 0.95 / Net I/σ(I): 19.5 / Num. measured all: 1013868
Reflection shell	Resolution: 1.62→1.66 Å / % possible obs: 93.4 % / Redundancy: 8.4 % / R_merge(I) obs: 0.953 / Num. measured all: 33558 / Num. unique obs: 3976 / CC_1/2: 0.778 / R_pim(I) all: 0.341 / R_rim(I) all: 1.014 / Χ²: 0.66 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5669: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.62→47.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1804	2923	4.98 %
R_work	0.1537	-	-
obs	0.1551	58687	98.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.62→47.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3501	0	84	370	3955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3719
X-RAY DIFFRACTION	f_angle_d	1.158	5048
X-RAY DIFFRACTION	f_dihedral_angle_d	18.282	1449
X-RAY DIFFRACTION	f_chiral_restr	0.059	551
X-RAY DIFFRACTION	f_plane_restr	0.011	641

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 (%)
1.62-1.65	0.2568	122	0.2729	2391	X-RAY DIFFRACTION	92
1.65-1.67	0.2663	118	0.2459	2477	X-RAY DIFFRACTION	94
1.68-1.71	0.2748	134	0.2258	2516	X-RAY DIFFRACTION	96
1.71-1.74	0.2518	127	0.1998	2541	X-RAY DIFFRACTION	97
1.74-1.77	0.2241	131	0.189	2603	X-RAY DIFFRACTION	99
1.77-1.81	0.2053	120	0.1707	2644	X-RAY DIFFRACTION	100
1.81-1.85	0.2083	150	0.1601	2625	X-RAY DIFFRACTION	100
1.85-1.9	0.1608	131	0.1559	2652	X-RAY DIFFRACTION	100
1.9-1.95	0.1784	149	0.1613	2646	X-RAY DIFFRACTION	100
1.95-2.01	0.217	138	0.1694	2630	X-RAY DIFFRACTION	100
2.01-2.07	0.1964	122	0.1672	2668	X-RAY DIFFRACTION	100
2.07-2.15	0.1763	153	0.1484	2647	X-RAY DIFFRACTION	100
2.15-2.23	0.1973	152	0.1428	2659	X-RAY DIFFRACTION	100
2.23-2.34	0.1852	135	0.1476	2683	X-RAY DIFFRACTION	100
2.34-2.46	0.1709	130	0.1464	2673	X-RAY DIFFRACTION	100
2.46-2.61	0.1943	170	0.1468	2668	X-RAY DIFFRACTION	100
2.61-2.82	0.1703	166	0.1509	2684	X-RAY DIFFRACTION	100
2.82-3.1	0.1582	146	0.1496	2730	X-RAY DIFFRACTION	100
3.1-3.55	0.1742	149	0.141	2766	X-RAY DIFFRACTION	100
3.55-4.47	0.1456	133	0.1255	2820	X-RAY DIFFRACTION	100
4.47-47.99	0.1766	147	0.161	3041	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	0.8085	0.1975	0.0159	0.7732	0.127	1.2702	-0.0398	-0.0059	0.0716	-0.0353	-0.0671	0.0629	-0.0955	-0.2329	0.0561	0.0979	0.0512	-0.007	0.1677	-0.0153	0.1725	3.3379	37.3483	19.5948
2	2.7574	0.5623	-1.0632	0.816	-0.7835	2.4114	-0.0004	0.1211	0.0966	-0.0373	-0.001	0.2138	-0.0017	-0.4475	-0.0659	0.0539	0.0358	-0.0011	0.5313	-0.0855	0.2726	-14.3203	34.7118	14.0246
3	1.1067	0.307	0.5138	1.6682	0.3958	3.5405	-0.2037	0.2254	-0.1872	-0.3913	0.0592	-0.0492	0.6341	-0.637	0.047	0.2713	-0.0743	0.0209	0.4974	-0.0469	0.278	-11.5148	27.7788	9.3236
4	0.1566	-0.0161	0.1267	0.9089	0.2992	1.33	-0.0123	0.0633	0.0449	-0.0493	-0.0339	0.0563	-0.0426	-0.1721	0.0645	0.0864	0.0341	-0.0131	0.1679	-0.0045	0.177	4.3071	32.0464	11.748
5	2.5624	-0.2752	-1.5015	1.2663	0.2842	1.5481	-0.012	0.1864	0.2473	-0.2049	-0.1771	0.1312	-0.3346	-0.3968	-0.1475	0.1979	0.1932	-0.1088	0.2929	-0.0575	0.2868	-6.7895	43.4583	9.8321
6	1.3959	-0.2911	0.3962	0.7013	0.1221	0.923	-0.1006	0.0236	0.2794	-0.1205	-0.0334	0.1496	-0.4494	-0.189	0.028	0.2689	0.095	-0.0571	0.1496	-0.0064	0.2291	6.8754	51.7271	19.0601
7	0.9816	-0.3706	0.1006	0.5431	-0.2886	0.7722	-0.0121	0.0533	-0.153	-0.0409	0.0286	0.007	0.8212	0.2485	0.0234	0.329	0.1989	0.0104	0.1499	-0.0067	0.1605	20.1788	9.8894	19.9382
8	1.5641	1.2206	0.8751	1.7908	2.0851	2.8477	-0.1392	0.7299	-0.1151	-0.6105	0.2044	-0.2023	0.1934	0.6082	-0.1242	0.6568	0.2607	0.0338	0.6175	-0.0503	0.2577	33.0196	3.022	9.6034
9	0.9065	0.1044	-0.0412	0.3071	-0.1574	0.8297	-0.0472	0.1164	-0.1025	-0.1021	0.0467	-0.0406	0.5909	0.2308	0.0175	0.279	0.0977	0.0044	0.1638	-0.0042	0.165	20.527	12.1306	12.3099
10	1.0864	0.0928	-0.536	1.5599	0.3584	1.1255	0.0225	-0.0053	-0.2696	0.1464	-0.1526	0.2386	0.7035	-0.2288	-0.0119	0.4339	-0.0977	0.0183	0.2045	0.0139	0.1887	4.375	8.38	22.7021
11	0.6827	-0.3389	-0.317	0.6192	-0.0824	1.1107	-0.0033	0.0284	-0.0157	-0.0135	-0.0088	-0.036	-0.1315	0.4918	-0.0376	0.1023	-0.0068	0.0002	0.2914	0.0149	0.1565	32.4279	37.7557	18.1939
12	1.9784	0.6903	-0.6911	2.7604	1.4611	2.7927	0.0778	0.4738	0.173	-0.8042	-0.1977	-0.1845	-1.0822	0.2018	0.0252	0.5086	-0.0866	0.0506	0.4557	0.0451	0.2354	35.8216	52.6738	5.0696
13	1.6417	0.6585	-0.4722	0.653	-1.7251	6.6012	0.0703	0.2707	0.2808	-0.3654	-0.0578	0.1525	-0.9861	0.135	-0.0081	0.5013	-0.0339	0.0387	0.3296	0.075	0.2819	30.2227	55.2939	10.011
14	1.1964	-0.4108	-0.0835	0.8462	0.3137	1.1628	0.0369	0.1208	-0.079	-0.1286	-0.042	0.0112	-0.1227	0.3565	0.0001	0.1031	-0.0066	0.0077	0.2348	0.0293	0.1497	27.379	38.3149	10.2189
15	0.7839	0.5755	0.0489	1.0166	1.0485	1.727	0.0571	0.061	0.2048	-0.1343	0.1026	-0.2522	-0.2779	0.5247	-0.0658	0.1452	-0.056	0.0152	0.4837	0.0184	0.218	42.6791	41.9467	7.5408
16	0.6984	-0.2471	0.0059	0.2576	-0.0435	0.3316	0.0012	-0.0174	-0.0737	-0.0241	0.0411	-0.1646	0.0759	0.4701	0.071	0.0921	0.1131	0.0222	0.573	-0.0125	0.2108	43.1428	27.5755	19.1842

Refinement TLS group

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

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