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

ID or keywords:

Entry

Database: PDB / ID: 9oba

Title

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum containing phosphorylated active site histidine

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: 1.58 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 containing phosphorylated active site histidine
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

-
Download

PDBx/mmCIF format	9oba.cif.gz	197.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9oba.ent.gz	156.8 KB	Display	PDB format
PDBx/mmJSON format	9oba.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/9oba ftp://data.pdbj.org/pub/pdb/validation_reports/ob/9oba	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

53.1 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)	69.665, 69.665, 315.755
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-272- HOH
2	1	A-320- HOH

#1: Protein	nucleoside-diphosphate kinase Mass: 17692.340 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.97 %
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. Crystals were soaked with 10mM ATP for 4 hours which phosphorylated His139. No ADP bound after phosphorylation. plate Liu-S-177 D2, Puck: PSL-0411, Cryo: direct

Crystal

Density Matthews: 2.08 Å³/Da / Density % sol: 40.97 %

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 ...

-
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: 1.58→47.93 Å / Num. obs: 63689 / % possible obs: 99.9 % / Redundancy: 16.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.03 / R_rim(I) all: 0.125 / Χ²: 0.89 / Net I/σ(I): 15.7 / Num. measured all: 1043431
Reflection shell	Resolution: 1.58→1.62 Å / % possible obs: 98.9 % / Redundancy: 6.3 % / R_merge(I) obs: 0.836 / Num. measured all: 28754 / Num. unique obs: 4551 / CC_1/2: 0.721 / R_pim(I) all: 0.35 / R_rim(I) all: 0.911 / Χ²: 0.68 / Net I/σ(I) obs: 1.8

-
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: 1.58→47.93 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1681	3037	4.78 %
R_work	0.144	-	-
obs	0.1451	63518	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.58→47.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3509	0	0	442	3951

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3662
X-RAY DIFFRACTION	f_angle_d	1.049	4964
X-RAY DIFFRACTION	f_dihedral_angle_d	15.305	1429
X-RAY DIFFRACTION	f_chiral_restr	0.059	541
X-RAY DIFFRACTION	f_plane_restr	0.01	643

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 (%)
1.58-1.6	0.3681	147	0.2858	2628	X-RAY DIFFRACTION	98
1.6-1.63	0.3265	131	0.2628	2682	X-RAY DIFFRACTION	99
1.63-1.66	0.2741	135	0.2322	2707	X-RAY DIFFRACTION	100
1.66-1.69	0.2194	136	0.1948	2654	X-RAY DIFFRACTION	100
1.69-1.72	0.2332	134	0.1752	2686	X-RAY DIFFRACTION	100
1.72-1.76	0.1864	134	0.1546	2703	X-RAY DIFFRACTION	100
1.76-1.8	0.1776	141	0.1419	2701	X-RAY DIFFRACTION	100
1.8-1.84	0.1623	150	0.1379	2720	X-RAY DIFFRACTION	100
1.84-1.88	0.1712	138	0.1315	2702	X-RAY DIFFRACTION	100
1.88-1.93	0.1612	150	0.1383	2694	X-RAY DIFFRACTION	100
1.93-1.99	0.176	126	0.1463	2714	X-RAY DIFFRACTION	100
1.99-2.05	0.1764	149	0.1499	2710	X-RAY DIFFRACTION	100
2.05-2.13	0.1536	139	0.1198	2727	X-RAY DIFFRACTION	100
2.13-2.21	0.1472	141	0.1209	2711	X-RAY DIFFRACTION	100
2.21-2.31	0.1548	105	0.1231	2803	X-RAY DIFFRACTION	100
2.31-2.44	0.1635	148	0.1283	2728	X-RAY DIFFRACTION	100
2.44-2.59	0.1615	142	0.1333	2767	X-RAY DIFFRACTION	100
2.59-2.79	0.1639	123	0.136	2815	X-RAY DIFFRACTION	100
2.79-3.07	0.1616	125	0.143	2801	X-RAY DIFFRACTION	100
3.07-3.51	0.1428	164	0.1376	2811	X-RAY DIFFRACTION	100
3.51-4.43	0.1177	139	0.1225	2895	X-RAY DIFFRACTION	100
4.43-47.93	0.1988	140	0.1611	3122	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	0.2939	0.1889	0.0203	0.2483	0.0504	0.3548	-0.0181	-0.0085	0.0414	-0.0329	-0.0179	0.0363	-0.01	-0.0266	0	0.1037	0.0187	-0.0018	0.116	-0.0025	0.1175	3.6701	36.9828	19.5753
2	0.0022	0.0012	-0.0142	0.0546	0.0009	0.0538	-0.1626	0.1731	0.2649	-0.0662	0.0357	0.1182	-0.0706	-0.2594	-0.0018	0.1177	-0.0093	-0.0185	0.2142	-0.0115	0.2054	-14.2012	34.9967	13.3091
3	0.2375	0.1972	-0.0098	0.2279	-0.0588	0.1349	-0.0995	0.2457	-0.1181	-0.3261	-0.1408	-0.2249	0.7633	-0.0326	-0.026	0.2687	-0.0215	0.0077	0.2622	-0.0461	0.1835	-11.6804	27.7964	8.7876
4	0.1423	-0.0327	0.0477	0.0062	-0.0276	0.1076	-0.0178	0.0195	-0.0097	-0.0822	-0.0259	0.0446	0.0159	-0.0062	-0	0.1251	0.0158	-0.0052	0.139	0.0029	0.1356	4.7381	39.1553	13.1494
5	0.0217	0.0701	0.0708	0.3624	0.2485	0.1557	0.0198	0.1109	-0.033	-0.0576	0.0358	0.0855	-0.0274	-0.0474	0.0014	0.1062	0.0179	-0.0139	0.1333	-0.0003	0.112	4.599	26.8357	10.8235
6	0.0682	0.0142	0.0446	0.0596	-0.0214	0.05	-0.0978	0.2028	0.1236	-0.2312	-0.0417	0.1843	0.0672	-0.1551	-0.0217	0.1705	0.0282	-0.0532	0.1573	0.0084	0.1945	-6.0723	43.1603	9.7522
7	0.1315	0.0603	0.0704	0.2567	0.1547	0.0314	-0.0104	0.0715	0.2545	-0.0816	0.0017	0.0928	-0.0836	-0.0098	-0.0182	0.1257	0.0267	-0.0178	0.1178	0.011	0.173	7.4608	51.4139	19.1279
8	0.0621	-0.0048	-0.0115	-0.0188	0.0062	0.18	-0.0562	0.0393	-0.0807	-0.017	0.0613	0.0029	0.0756	0.0348	-0.0111	0.1263	0.0391	-0.0038	0.1326	0.0042	0.1211	22.0671	10.962	18.924
9	0.2102	-0.23	-0.0447	0.0541	0.1124	0.2214	-0.0209	-0.0511	-0.0241	-0.0281	0.0212	0.006	0.0641	0.0037	-0.0001	0.1211	0.0225	-0.0035	0.1265	0.011	0.1278	16.6311	12.8026	22.1783
10	0.0506	0.0149	-0.0526	0.0112	-0.019	0.0719	0.2141	0.0766	-0.0763	-0.1823	-0.0934	0.0282	0.2002	0.1175	0.0075	0.2258	0.081	-0.0203	0.1283	-0.009	0.1702	29.3238	-2.8166	14.2854
11	0.2636	0.0534	-0.1356	1.5783	-0.5054	0.2338	0.0873	0.342	0.0004	-0.2524	0.222	0.1986	-0.1701	0.311	0.0872	0.2892	0.05	-0.018	0.2707	-0.0418	0.1495	32.1488	1.1784	4.7753
12	0.0268	0.0029	-0.0219	0.009	0.0116	0.0292	0.1177	0.3423	0.1767	-0.4166	-0.0456	-0.165	-0.0782	0.153	-0.0017	0.2245	0.0633	0.0426	0.2257	-0.0057	0.1634	35.8863	4.2254	13.5933
13	0.1481	-0.0879	-0.0862	0.0442	0.0593	0.0928	-0.0517	-0.0041	-0.0208	-0.0397	0.0494	0.0236	0.0491	-0.0358	-0.0014	0.137	0.0236	-0.0153	0.1257	0.0005	0.1291	15.9155	11.3653	14.6386
14	0.3643	0.232	-0.2118	0.0702	0.0598	0.2193	0.0518	0.1468	-0.0011	-0.1046	0.0052	-0.0411	0.0136	0.0896	0.0016	0.1365	0.027	-0.0027	0.124	-0.0079	0.109	26.1876	17.0944	10.6642
15	0.0456	-0.0179	-0.0484	0.0297	-0.0282	0.1316	0.0503	0.0575	-0.2586	-0.0874	-0.2092	0.0978	0.4367	0.0951	-0.0081	0.2436	0.0286	0.0087	0.1323	-0.0398	0.2223	18.1805	-0.4171	11.486
16	0.3496	0.1412	-0.3255	0.2273	0.0173	0.2627	0.013	0.0214	-0.2327	-0.1272	-0.0912	0.238	0.1014	-0.0992	-0.0332	0.1552	-0.0178	0.0088	0.1294	0.0048	0.1673	4.6405	8.4471	22.0677
17	0.0847	-0.0798	0.0353	0.2357	0.2465	0.5797	0.013	-0.01	0.0577	-0.0126	-0.013	-0.0748	-0.0666	0.0857	-0.0014	0.0956	0.0089	0.0091	0.1386	0.0069	0.1295	34.2539	40.3562	16.8523
18	0.121	0.0084	0.0798	0.1379	-0.0819	0.119	0.0434	0.3414	0.2517	0.0223	-0.0028	0.1459	-0.0395	-0.5692	-0.0137	0.1851	0.0339	0.0256	0.2863	0.0843	0.1887	32.5211	54.1027	5.6357
19	0.0269	0.0893	-0.0473	0.1528	-0.0868	0.1261	-0.0115	0.0607	0.042	-0.0634	0.0193	-0.005	-0.0031	0.0661	-0	0.1093	0.0153	0.0158	0.1492	0.0077	0.1187	34.3263	34.435	12.1362
20	0.2631	-0.2663	0.1957	0.1012	-0.1347	0.1513	0.0591	0.1279	0.0423	-0.0958	0.0074	0.0276	-0.0707	0.0528	0.0006	0.1218	0.0053	0.0118	0.1514	0.0175	0.1251	23.7406	40.7465	9.0904
21	0.0434	0.0903	-0.0416	0.0984	-0.0378	0.0395	0.0248	0.2244	0.1455	-0.2528	0.1262	-0.2126	-0.2571	0.1501	0	0.128	-0.0083	0.0164	0.1895	0.0194	0.1646	43.1313	41.7655	7.7201
22	0.2231	-0.0846	0.2273	0.1784	-0.2835	0.214	-0.0496	0.0417	-0.1438	-0.1461	0.022	-0.3647	0.0506	0.0842	-0.0081	0.1072	0.0282	0.0173	0.1773	-0.0036	0.1516	43.5978	27.3162	19.2621

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 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 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 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 65 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 73 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 74 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 113 through 143 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 144 through 154 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 155 through 173 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 25 through 73 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 74 through 92 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 93 through 112 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 113 through 143 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 144 through 154 )
22	X-RAY DIFFRACTION	22	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