PDB-4di6: crystal structure of nucleoside-diphosphate kinase from Borrelia ...

ID or keywords:

Entry

Database: PDB / ID: 4di6

Title

crystal structure of nucleoside-diphosphate kinase from Borrelia burgdorferi

Components

Nucleoside diphosphate kinase

Keywords

TRANSFERASE / SSGCID / NUCLEOSIDE DIPHOSPHATE KINASE / KINASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Function and homology information

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

Biological species

Borrelia burgdorferi (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
Authors: Dumais, M. / Davies, D.R. / Lin, T. / Staker, B.L. / Myler, P.J. / Van Voorhis, W.C.

History

Deposition	Jan 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4di6.cif.gz	403.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4di6_validation.pdf.gz	465 KB	Display	wwPDB validaton report
Full document	4di6_full_validation.pdf.gz	469.9 KB	Display
Data in XML	4di6_validation.xml.gz	39 KB	Display
Data in CIF	4di6_validation.cif.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/di/4di6 ftp://data.pdbj.org/pub/pdb/validation_reports/di/4di6	HTTPS FTP

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Related structure data

Related structure data	4dz6C C: citing same article (ref.)
Similar structure data	4dz6-d 5bxi-1 1409 3bbc-d 6joh-2 5n0k-d 1s57-d 3mpd-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BobuA.00664.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleoside diphosphate kinase

B: Nucleoside diphosphate kinase

C: Nucleoside diphosphate kinase

D: Nucleoside diphosphate kinase

E: Nucleoside diphosphate kinase

F: Nucleoside diphosphate kinase

130 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	135.260, 135.260, 126.650
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase Mass: 21693.934 Da / Num. of mol.: 6 / Fragment: NUCLEOSIDE-DIPHOSPHATE KINASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: ndk, BB_0463 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O51419, nucleoside-diphosphate kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase

Mass: 21693.934 Da / Num. of mol.: 6 / Fragment: NUCLEOSIDE-DIPHOSPHATE KINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Borrelia burgdorferi (Lyme disease spirochete)
Gene: ndk, BB_0463 / Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O51419, nucleoside-diphosphate kinase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.86 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS INTERNAL TRACKING NUMBER 8.5, 20% PEG 3500. BOBUA.00664.A.A1 PS00257 AT 17 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, pH 8.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 50359 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 32.59 Å² / R_merge(I) obs: 0.109 / Net I/σ(I): 15.33
Reflection shell	Resolution: 2.4→2.46 Å / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 4.2 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.6.0117	refinement
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→46.22 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.902 / SU B: 12.634 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	2557	5.1 %	RANDOM
R_work	0.175	-	-	-
obs	0.177	50334	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 25.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	-0.2 Å²	0 Å²
2-	-	-0.39 Å²	0 Å²
3-	-	-	0.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→46.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8048	0	0	431	8479

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	8293
X-RAY DIFFRACTION	r_angle_refined_deg	1.259	1.95	11225
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.801	5	1023
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.531	23.594	384
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.016	15	1452
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.922	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1238
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	6244

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	197	-
R_work	0.213	3513	-
obs	-	-	99.2 %

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	0.2718	0.0877	-0.2281	3.1348	-1.2351	0.8246	-0.0753	0.0153	-0.0453	-0.0291	0.0544	-0.0159	0.0017	0.0091	0.0208	0.1333	-0.0327	0.0227	0.1449	-0.0276	0.1514	49.46	6.7938	108.6116
2	0.412	-0.6158	0.3592	2.7329	-0.0168	0.4895	-0.0539	-0.0065	0.0164	-0.1089	0.0636	-0.129	-0.0364	-0.0075	-0.0097	0.1558	-0.0466	0.0554	0.1765	-0.0106	0.1512	46.944	4.0612	105.2148
3	3.5674	1.6817	1.0303	2.3976	-1.1015	1.8763	-0.0992	0.1405	-0.0867	-0.1223	0.0068	-0.1093	0.0519	0.097	0.0924	0.1309	0.0224	0.0743	0.1522	-0.0645	0.1781	66.9654	-1.4514	104.15
4	0.6628	-0.476	0.3112	0.7682	-0.1879	0.2062	-0.0889	-0.0542	0.0524	-0.0883	0.0076	-0.1166	-0.0354	0.034	0.0812	0.1384	-0.0065	0.0439	0.1717	-0.0086	0.18	55.6358	8.5592	113.6801
5	1.2913	-0.5726	0.8955	0.9379	-0.4091	0.8196	-0.094	0.049	-0.0525	-0.06	0.0191	-0.0901	0.0118	-0.0013	0.0749	0.1313	-0.015	0.0606	0.1569	-0.0269	0.1361	56.9301	3.4977	104.1171
6	1.5694	1.2278	0.1524	7.7622	2.2803	0.7034	0.1041	0.1619	0.178	-0.3574	-0.1258	0.1561	-0.1173	-0.0824	0.0217	0.1972	-0.0545	-0.018	0.1706	0.0562	0.1236	37.4797	19.4918	100.7026
7	0.1373	-0.2404	0.337	2.2507	-0.8974	1.1353	-0.0653	0.0249	-0.0034	0.0056	-0.0174	0.0202	0.0347	-0.0313	0.0827	0.1641	-0.0382	0.0449	0.1456	-0.0366	0.1516	34.4537	-1.7448	112.1645
8	0.3096	-0.308	-0.2861	0.8859	0.2103	0.2983	-0.086	0.0574	-0.0709	-0.098	-0.056	-0.0668	0.0656	-0.0571	0.1421	0.2066	-0.0642	0.0001	0.1359	-0.0649	0.1871	32.3284	-3.7317	98.4266
9	9.3672	4.7678	1.2133	7.3623	2.1084	1.9607	-0.195	-0.1349	0.1535	0.1115	-0.2154	0.2899	0.0685	-0.2239	0.4104	0.1315	-0.0588	0.0234	0.201	-0.0834	0.0973	18.5025	-2.1375	96.8912
10	0.8927	0.3848	-0.4694	1.8587	-3.1152	5.2996	-0.079	0.1016	-0.0631	-0.152	0.0162	-0.0022	0.2663	-0.0548	0.0628	0.2411	-0.0804	0.0513	0.1027	-0.0791	0.1477	32.9047	-6.3538	111.19
11	0.9451	-0.541	0.1506	2.488	-1.1547	2.2038	-0.0567	0.0424	0.0049	-0.1595	0.1456	0.1556	0.1203	-0.2402	-0.0889	0.139	-0.0745	-0.0114	0.1616	-0.015	0.1724	20.1974	6.4176	111.683
12	0.874	0.0614	0.7032	1.1345	0.2946	1.9578	-0.0432	0.0361	-0.1876	-0.0987	0.0089	0.0111	0.2167	0.0372	0.0342	0.1774	-0.0483	0.0618	0.0671	-0.0266	0.1354	37.2031	-10.6444	110.0829
13	0.5992	0.2385	0.1658	0.727	0.3661	1.4631	0.0159	-0.047	0.0289	-0.0629	0.0881	-0.0191	0.0347	-0.0415	-0.104	0.1536	-0.0239	0.0092	0.1327	0.0061	0.1656	24.4591	20.2511	125.2221
14	2.9027	0.5656	-0.6731	0.9239	0.5251	3.4885	0.1545	-0.1487	0.3509	-0.0307	0.1703	0.0913	-0.2296	-0.0505	-0.3248	0.1138	0.0392	0.0362	0.1127	0.0494	0.1999	17.2251	30.987	130.7367
15	13.9181	-1.1312	-1.5051	8.7187	1.4061	0.3543	0.2361	0.2276	-0.4529	-0.1564	-0.3122	0.4778	-0.0494	-0.0709	0.0761	0.1129	0.0006	-0.0195	0.1743	0.0574	0.1675	3.8446	22.1933	140.3991
16	1.0352	-0.1134	-1.0636	0.6895	0.1489	1.2279	0.0029	0.0423	0.0785	-0.0307	0.0373	0.0802	-0.0779	-0.1464	-0.0401	0.1079	0.0063	-0.001	0.1419	0.0141	0.1826	17.2274	23.1155	129.9743
17	0.1666	0.0937	-0.0623	0.6688	-0.6544	1.5637	-0.0303	-0.0068	0.0359	0.0676	0.0873	0.0765	0.0356	-0.1577	-0.0571	0.0991	-0.0086	0.0166	0.1734	0.0016	0.177	18.0965	18.5267	132.2571
18	0.8735	3.2591	0.4558	14.4893	3.2859	1.3337	-0.1096	0.1448	0.0792	-0.5796	-0.0904	0.4823	-0.2092	-0.3228	0.2	0.1024	-0.0199	-0.0572	0.2454	0.0127	0.1296	23.7071	19.7113	106.4774
19	2.9501	-0.8296	-1.7675	0.4064	0.757	1.4529	0.0199	-0.1397	0.0337	-0.0114	0.009	-0.0104	-0.0217	0.062	-0.0288	0.1376	-0.0144	-0.014	0.1671	0.0267	0.1469	52.1722	9.6547	137.3319
20	1.0158	0.5407	-0.7641	0.9393	-0.2324	0.6354	0.0285	-0.1821	-0.1004	0.1252	-0.1211	-0.0737	0.0452	0.1027	0.0926	0.1055	-0.0077	-0.0343	0.213	0.0134	0.1566	54.5778	9.7793	145.9725
21	7.5161	-5.0265	10.2015	9.5809	-5.4799	15.3722	-0.2783	1.2917	1.2086	0.7383	-0.819	-2.0175	0.0605	1.3665	1.0973	0.1408	-0.1807	-0.1591	0.5129	0.1556	0.5648	65.4046	25.0843	149.3892
22	0.4147	0.3744	-0.3306	1.3572	0.9832	1.9242	-0.0138	-0.1495	-0.0033	0.0762	-0.039	-0.0358	0.1182	0.2439	0.0528	0.0819	-0.0001	-0.0326	0.2139	0.0014	0.1629	55.8938	13.7255	142.3456
23	0.2893	-0.2022	0.0083	1.166	0.0461	0.4322	-0.013	-0.1194	0.0819	0.0035	0.048	-0.0465	-0.0729	0.1783	-0.035	0.1023	-0.0215	-0.0109	0.2054	-0.0316	0.1621	55.0046	18.9929	139.5978
24	1.4138	1.0199	-0.1755	0.8779	-0.356	4.1574	-0.1934	-0.0296	-0.1963	-0.0587	0.0299	-0.0638	0.26	0.062	0.1635	0.1262	0.0675	0.0535	0.0973	0.0286	0.2047	56.337	-5.4538	130.3993
25	1.9929	-0.9176	-1.1426	1.0142	0.2427	0.8305	-0.0471	-0.084	-0.0811	-0.0165	-0.0299	-0.0302	0.0911	0.0202	0.077	0.1406	-0.0131	0.0029	0.1369	-0.0059	0.1593	37.4804	-0.2243	139.1279
26	0.9769	0.4973	0.361	0.9344	0.4549	0.2591	0.0131	-0.1533	-0.0228	0.129	-0.0251	-0.0841	0.0404	-0.0085	0.012	0.1742	-0.0186	0.0345	0.1588	0.0438	0.1538	40.3174	-4.2633	144.4917
27	5.1803	2.8234	-0.7704	1.5525	-0.5866	2.5429	-0.0314	-0.1822	-0.102	-0.0248	-0.0869	-0.0828	0.0884	-0.1308	0.1183	0.1817	0.0202	0.0231	0.0954	0.0244	0.1951	34.2037	-20.7657	142.4226
28	3.0851	-1.172	-0.081	2.0153	0.1566	0.3178	-0.1245	-0.1685	-0.036	0.138	0.0453	0.027	0.1049	-0.0512	0.0791	0.158	-0.0101	0.0339	0.1455	0.0359	0.1185	34.513	-0.7849	142.5046
29	0.3865	0.3652	0.2896	0.5974	0.0087	0.7926	-0.0839	-0.0398	-0.0239	-0.0482	0.0158	0.0167	0.1016	-0.0629	0.0681	0.185	-0.0093	0.0596	0.1238	-0.0012	0.1611	33.5284	-8.9897	135.6639
30	3.3678	-1.8892	1.7316	1.3979	-0.9546	1.842	-0.0349	-0.3069	-0.0105	0.1405	0.1179	0.1475	-0.0998	0.0871	-0.083	0.1344	-0.0248	0.0364	0.1993	-0.0326	0.1148	34.4866	13.331	149.0672
31	0.5588	-0.1092	0.6397	0.1716	0.322	2.4501	0.0225	0.0157	-0.0163	-0.0994	0.0133	-0.0396	-0.0851	0.0157	-0.0358	0.156	-0.0316	0.0248	0.122	0.001	0.1765	37.3933	30.1009	121.2617
32	0.7831	0.3969	-0.2178	0.2111	-0.0794	0.1861	0.018	0.0193	0.1162	0.0026	0.0377	0.0574	-0.0284	0.0295	-0.0557	0.1709	-0.013	0.0281	0.1254	-0.0252	0.1787	34.852	35.982	119.2698
33	4.6654	0.3549	0.3203	9.7978	-1.9348	6.7679	0.1003	-0.3696	0.0329	0.1583	-0.1667	-0.2917	-0.3052	0.1288	0.0664	0.1236	-0.0654	0.0393	0.0949	-0.0165	0.1875	47.1359	46.2504	107.5037
34	0.4519	-0.0239	-0.1165	0.3842	-0.7591	1.6344	-0.0656	-0.0364	0.1171	0.0236	0.0553	-0.069	-0.1185	-0.0916	0.0103	0.1843	-0.0191	0.025	0.0911	-0.0116	0.1992	39.387	35.4005	117.8289
35	0.5135	-0.2977	-0.1288	1.3938	0.1793	0.439	0.0251	0.013	0.0458	0.0288	-0.0151	-0.0931	-0.0132	0.0986	-0.0099	0.1484	-0.0486	0.0253	0.1296	-0.0161	0.1737	45.5413	30.4934	112.3245
36	1.3038	-0.7168	-0.2432	1.1803	-0.7997	1.2408	-0.0602	-0.1695	0.1088	0.1762	0.1564	0.0128	-0.1732	-0.1234	-0.0962	0.1613	-0.0373	0.0139	0.1304	-0.0582	0.183	34.7955	34.6465	134.3555

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 29
2	X-RAY DIFFRACTION	2	A	30 - 47
3	X-RAY DIFFRACTION	3	A	48 - 75
4	X-RAY DIFFRACTION	4	A	76 - 122
5	X-RAY DIFFRACTION	5	A	123 - 157
6	X-RAY DIFFRACTION	6	A	158 - 170
7	X-RAY DIFFRACTION	7	B	2 - 35
8	X-RAY DIFFRACTION	8	B	36 - 55
9	X-RAY DIFFRACTION	9	B	56 - 77
10	X-RAY DIFFRACTION	10	B	78 - 95
11	X-RAY DIFFRACTION	11	B	96 - 131
12	X-RAY DIFFRACTION	12	B	132 - 170
13	X-RAY DIFFRACTION	13	C	5 - 35
14	X-RAY DIFFRACTION	14	C	36 - 55
15	X-RAY DIFFRACTION	15	C	56 - 66
16	X-RAY DIFFRACTION	16	C	67 - 95
17	X-RAY DIFFRACTION	17	C	96 - 157
18	X-RAY DIFFRACTION	18	C	158 - 170
19	X-RAY DIFFRACTION	19	D	2 - 30
20	X-RAY DIFFRACTION	20	D	31 - 56
21	X-RAY DIFFRACTION	21	D	57 - 66
22	X-RAY DIFFRACTION	22	D	67 - 96
23	X-RAY DIFFRACTION	23	D	97 - 154
24	X-RAY DIFFRACTION	24	D	155 - 170
25	X-RAY DIFFRACTION	25	E	3 - 29
26	X-RAY DIFFRACTION	26	E	30 - 55
27	X-RAY DIFFRACTION	27	E	56 - 75
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