PDB-3czq: Crystal structure of putative polyphosphate kinase 2 from Sinorhi...

ID or keywords:

Entry

Database: PDB / ID: 3czq

Title

Crystal structure of putative polyphosphate kinase 2 from Sinorhizobium meliloti

Components

Putative polyphosphate kinase 2

Keywords

TRANSFERASE / structural genomics / APC6299 / polyphosphate kinase 2 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / ATP biosynthetic process / phosphorylation / identical protein binding
Similarity search - Function

Biological species

Sinorhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.23 Å

Authors

Osipiuk, J. / Evdokimova, E. / Nocek, B. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria.
Authors: Nocek, B. / Kochinyan, S. / Proudfoot, M. / Brown, G. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F.

History

Deposition	Apr 29, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3czq.cif.gz	242.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3czq.ent.gz	208.1 KB	Display	PDB format
PDBx/mmJSON format	3czq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3czq_validation.pdf.gz	482.6 KB	Display	wwPDB validaton report
Full document	3czq_full_validation.pdf.gz	508 KB	Display
Data in XML	3czq_validation.xml.gz	44.6 KB	Display
Data in CIF	3czq_validation.cif.gz	62.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cz/3czq ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czq	HTTPS FTP

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Related structure data

Related structure data	3czpC C: citing same article (ref.)
Similar structure data	6dzg-d 6waz-d 2oa6-d 3uer-1 1rtd-2 1mda-d 1xr2-d 4yao-d 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	TargetDB: APC6299

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative polyphosphate kinase 2

B: Putative polyphosphate kinase 2

C: Putative polyphosphate kinase 2

D: Putative polyphosphate kinase 2

hetero molecules

143 kDa, 4 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)	59.609, 71.672, 89.471
Angle α, β, γ (deg.)	75.86, 85.97, 65.39
Int Tables number	1
Space group name H-M	P1

#1: Protein	Putative polyphosphate kinase 2 Mass: 35663.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00507, SMc02148 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92SA6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.36 Å³/Da / Density % sol: 47.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium formate, 0.1 M Lithium sulfate, 0.1 M Bis-tris buffer, 0.3 M NDSB-211, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2007
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.23→34.7 Å / Num. all: 56568 / Num. obs: 56568 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 59.8 Å² / R_merge(I) obs: 0.066 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.23→2.31 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.381 / Mean I/σ(I) obs: 1.99 / % possible all: 46.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.23→34.7 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.938 / SU B: 14.972 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2403	2840	5 %	RANDOM
R_work	0.18696	-	-	-
obs	0.18968	56551	89.28 %	-
all	-	56551	-	-

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: 57.022 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	-0.19 Å²	0.04 Å²
2-	-	0.74 Å²	0.52 Å²
3-	-	-	-0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.23→34.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9418	0	12	255	9685

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	9687
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.945	13054
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.048	5	1145
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.533	23.012	508
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.879	15	1728
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.377	15	99
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1325
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7489
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	4364
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	6361
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	436
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.301	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.187	0.2	4
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.746	1.5	5859
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.198	2	9177
X-RAY DIFFRACTION	r_scbond_it	1.937	3	4397
X-RAY DIFFRACTION	r_scangle_it	2.971	4.5	3876
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.23→2.29 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	101	-
R_work	0.248	1935	-
obs	-	-	43.75 %

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	5.2464	-0.5303	-1.0908	1.0653	-0.0321	3.3097	-0.1626	-0.2577	0.1648	0.1623	0.0182	-0.1685	-0.1009	0.6415	0.1444	-0.1993	-0.0497	-0.0595	0.0969	0.0071	-0.1813	78.716	28.6362	67.7823
2	0.4781	-0.2479	0.8316	0.1975	-0.0861	3.1752	0.0326	0.0547	-0.0422	0.0092	-0.0499	-0.0189	0.2767	-0.254	0.0173	-0.1443	-0.0687	0.0064	0.0405	0.0077	-0.059	55.812	23.8814	50.7906
3	9.3402	1.9543	-0.1683	3.4447	-0.0715	0.3786	-0.1455	-0.1093	-0.0496	-0.1186	-0.0032	-0.2897	-0.0777	0.8891	0.1488	-0.113	-0.0778	-0.0167	0.2162	0.0662	-0.0855	70.8614	30.8783	41.4915
4	2.0968	-0.2805	1.2784	0.3039	0.0397	3.3026	-0.1777	0.0218	0.1483	-0.0348	0.0205	-0.0295	-0.4706	0.1074	0.1571	-0.1468	-0.0716	-0.0088	-0.0372	0.0471	-0.0447	64.5156	33.3092	50.7552
5	2.5357	1.5658	-1.099	9.271	-2.2746	3.3374	-0.1435	0.3786	-0.159	-0.3658	-0.2388	0.1278	0.4064	0.8208	0.3823	-0.1968	0.0447	0.0168	0.1951	-0.0051	-0.1152	79.4086	19.8206	57.1633
6	1.2285	0.1827	0.5141	0.5453	-0.082	3.2545	-0.2209	-0.183	0.2846	-0.0155	0.0486	0.0182	-0.407	-0.0926	0.1723	-0.1195	-0.0332	-0.0302	-0.08	-0.0168	-0.0388	60.6562	35.6676	59.0528
7	4.7546	2.6501	-4.7102	4.4665	0.0746	14.4721	-0.1393	-0.1292	0.7551	-0.0999	0.0032	0.0601	-1.7625	0.1087	0.1362	-0.0321	-0.0219	-0.0986	-0.1945	-0.0497	-0.0071	64.094	41.4844	63.0208
8	4.03	0.51	0.1148	1.0466	-0.3102	3.0313	-0.1302	0.4382	0.3678	-0.0549	-0.0362	0.1932	0.009	-0.5967	0.1664	-0.2568	0.0471	-0.0322	0.1284	-0.0098	-0.1039	29.0842	28.0631	4.6932
9	0.6103	0.2215	1.0942	0.0919	0.2611	3.5781	0.0561	0.0626	0.0344	0.0641	-0.0346	-0.0092	0.2934	0.277	-0.0215	-0.1591	0.0497	0.0041	0.0375	0.0189	-0.0292	51.8425	23.6731	21.6998
10	7.9949	-3.6653	0.1884	2.6092	1.6773	3.3535	-0.4056	-0.3087	-0.2922	0.1271	0.0128	0.4279	0.0066	-0.6963	0.3928	-0.1826	0.0289	0.0092	0.1328	-0.0227	0.0444	37.2199	31.3667	31.3375
11	1.1978	0.2611	1.1151	0.0648	0.3589	3.8619	-0.1698	0.079	0.2987	0.0041	-0.0362	0.0502	-0.4407	-0.1338	0.206	-0.169	0.0639	-0.0201	-0.0568	0.0124	0.028	43.2243	32.8359	20.8373
12	6.959	-5.2415	1.0069	5.4959	-3.7634	5.9787	-0.6455	0.6832	0.1637	0.3866	0.142	0.0454	0.5444	-0.4896	0.5034	-0.1679	-0.0679	0.0505	0.0791	-0.0304	-0.0633	29.9225	14.9999	13.548
13	9.2692	4.5307	4.5496	2.2364	2.4862	5.3807	-0.1328	-0.5906	0.2767	0.2105	-0.2108	-0.182	-0.3937	-0.9818	0.3436	-0.1499	0.1614	-0.055	0.0338	-0.0596	0.0402	34.7387	36.1688	22.7426
14	2.8268	-0.3363	0.4573	0.6358	0.3121	2.9632	-0.2295	0.4519	0.3688	-0.0397	0.049	-0.0317	-0.3923	0.3301	0.1805	-0.1627	-0.0231	-0.0295	0.0608	0.1357	0.0097	49.4033	34.586	8.0381
15	4.3857	-0.4635	-0.3373	3.7911	-0.3995	2.6934	0.2982	-0.4258	-0.2217	0.642	-0.0888	0.4143	1.0363	-0.6633	-0.2094	0.3367	-0.4264	0.0815	-0.0102	0.0501	-0.2448	47.9969	-0.5631	76.4951
16	0.2528	0.0046	0.7141	0.9005	-0.1164	3.4253	0.2154	0.019	0.0685	-0.1065	-0.1473	-0.1058	0.9613	-0.139	-0.0681	0.1866	-0.0887	0.0849	-0.2163	-0.0045	-0.1185	58.1872	4.3886	50.7446
17	5.2187	0.2852	-1.3443	1.5617	-3.2633	25.0223	0.9399	-0.5995	0.5475	0.7442	-0.3937	0.5834	1.127	-0.6425	-0.5462	0.383	-0.4937	-0.0396	0.1171	0.1748	0.0857	38.1328	-2.4939	49.915
18	0.7344	0.0254	0.1867	1.0286	-0.1004	4.309	0.2666	-0.1073	-0.1108	-0.1533	-0.0502	0.0916	1.5115	-0.4836	-0.2165	0.5342	-0.288	-0.0218	-0.1754	0.0368	-0.1566	50.3359	-5.051	54.0201
19	0.9689	3.677	-0.0596	15.6157	2.7561	5.3592	0.2533	-0.4472	0.3767	0.358	-0.3357	1.1034	0.6756	-1.0385	0.0824	-0.1028	-0.2197	0.1294	0.0485	0.0494	-0.0181	43.4706	13.1921	68.1941
20	1.8359	0.9863	0.1346	1.9802	0.0306	3.5755	0.2435	-0.1753	-0.0784	-0.1624	-0.002	0.1062	1.3739	-0.3679	-0.2415	0.5476	-0.2216	-0.0389	-0.2747	0.0842	-0.1338	53.1013	-6.0748	60.5428
21	5.2676	2.4455	-3.386	6.9551	-3.0378	2.6333	-0.39	0.2175	-1.167	-0.5323	0.1864	-0.7101	1.5764	0.1835	0.2036	0.5363	0.0276	-0.0014	-0.2008	0.0566	-0.113	64.3748	-10.0878	65.2412
22	5.4666	-4.1372	2.5292	11.3963	5.0598	17.8716	0.0855	0.86	-0.3835	0.7057	0.2265	-1.0065	2.5432	0.4528	-0.312	0.2819	0.3965	-0.0683	0.559	-0.1305	-0.0705	74.9167	0.6165	-1.3825
23	3.1224	0.6477	-1.477	1.1981	0.9679	4.7365	0.2732	0.4557	-0.1575	0.203	-0.2131	0.0646	0.896	-0.0584	-0.0601	0.2014	0.1936	-0.0213	-0.146	-0.01	-0.2692	48.7655	-0.5094	1.0393
24	0.2192	-0.0921	0.8714	0.3309	-0.1517	3.6224	0.3128	0.0707	0.1827	0.0666	-0.2745	-0.0662	0.8932	0.0892	-0.0383	0.2311	0.0618	0.1127	-0.1456	0.0137	-0.1328	51.2799	4.781	24.5664
25	10.5193	-3.1785	-0.3208	2.2723	1.4589	1.4237	0.753	0.7073	0.3308	0.4509	-0.1681	-0.2375	1.0553	0.8184	-0.5849	0.5991	0.4261	-0.0673	0.0669	-0.0116	-0.1803	64.9499	-2.5442	24.7578
26	0.6254	0.2984	0.1903	0.1599	0.3556	4.0632	0.2543	0.1535	-0.0154	0.2395	-0.0158	-0.0299	1.298	0.5112	-0.2385	0.3834	0.2839	-0.0134	-0.1124	-0.0046	-0.1831	57.927	-0.5142	14.9196
27	2.3933	-0.4262	-0.4643	0.5515	0.4889	3.8913	0.2256	0.1525	-0.1011	0.5588	-0.081	-0.0706	1.5691	0.3311	-0.1446	0.6561	0.2397	-0.0354	-0.2319	-0.0464	-0.1937	54.0912	-5.2789	13.2272
28	14.0292	-4.1405	-9.0592	9.6762	4.3396	6.1781	0.0063	-1.432	-1.0901	0.6317	-0.1712	-0.4605	1.8877	0.2973	0.1648	0.9659	0.0748	-0.0112	-0.1304	-0.0124	-0.1204	47.4811	-11.7098	8.1807

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	12 - 66	14 - 68
2	X-RAY DIFFRACTION	2	A	A	67 - 147	69 - 149
3	X-RAY DIFFRACTION	3	A	A	148 - 170	150 - 172
4	X-RAY DIFFRACTION	4	A	A	171 - 207	173 - 209
5	X-RAY DIFFRACTION	5	A	A	208 - 230	210 - 232
6	X-RAY DIFFRACTION	6	A	A	231 - 286	233 - 288
7	X-RAY DIFFRACTION	7	A	A	287 - 299	289 - 301
8	X-RAY DIFFRACTION	8	B	B	13 - 66	15 - 68
9	X-RAY DIFFRACTION	9	B	B	67 - 147	69 - 149
10	X-RAY DIFFRACTION	10	B	B	148 - 172	150 - 174
11	X-RAY DIFFRACTION	11	B	B	173 - 207	175 - 209
12	X-RAY DIFFRACTION	12	B	B	208 - 221	210 - 223
13	X-RAY DIFFRACTION	13	B	B	222 - 249	224 - 251
14	X-RAY DIFFRACTION	14	B	B	250 - 299	252 - 301
15	X-RAY DIFFRACTION	15	C	C	16 - 67	18 - 69
16	X-RAY DIFFRACTION	16	C	C	68 - 152	70 - 154
17	X-RAY DIFFRACTION	17	C	C	153 - 167	155 - 169
18	X-RAY DIFFRACTION	18	C	C	168 - 207	170 - 209
19	X-RAY DIFFRACTION	19	C	C	208 - 221	210 - 223
20	X-RAY DIFFRACTION	20	C	C	222 - 277	224 - 279
21	X-RAY DIFFRACTION	21	C	C	278 - 299	280 - 301
22	X-RAY DIFFRACTION	22	D	D	14 - 34	16 - 36
23	X-RAY DIFFRACTION	23	D	D	35 - 76	37 - 78
24	X-RAY DIFFRACTION	24	D	D	77 - 145	79 - 147
25	X-RAY DIFFRACTION	25	D	D	146 - 172	148 - 174
26	X-RAY DIFFRACTION	26	D	D	173 - 217	175 - 219
27	X-RAY DIFFRACTION	27	D	D	218 - 282	220 - 284
28	X-RAY DIFFRACTION	28	D	D	283 - 299	285 - 301

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