PDB-6dzg: Crystal structure of polyphosphate kinase 2 class I (SMc02148) in...

ID or keywords:

Entry

Database: PDB / ID: 6dzg

Title

Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP

Components

Polyphosphate:ADP phosphotransferase 1

Keywords

TRANSFERASE / kinase / Structural Genomics / PSI-Biology / 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 / identical protein binding
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Nocek, B. / Joachimiak, A. / Ruszkowski, M. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Structural insights into substrate selectivity and activity of bacterial polyphosphate kinases
Authors: Nocek, B. / Joachimiak, A. / Yakunin, A. / Ruszkowski, M.

History

Deposition	Jul 3, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dzg.cif.gz	498.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6dzg.ent.gz	413.6 KB	Display	PDB format
PDBx/mmJSON format	6dzg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6dzg_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6dzg_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6dzg_validation.xml.gz	48.3 KB	Display
Data in CIF	6dzg_validation.cif.gz	67.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dz/6dzg ftp://data.pdbj.org/pub/pdb/validation_reports/dz/6dzg	HTTPS FTP

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Related structure data

Related structure data	3czqS S: Starting model for refinement
Similar structure data	3czq-d 2oa6-d 3nzp-d 1mda-d 6lgg-d 6pqn-d 3eps-d 3c75-d 5nsl-d 2j57-1 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: MCSG-APC6299

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (2) #21 - Sep 2001 Antibodies similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Polyphosphate:ADP phosphotransferase 1

B: Polyphosphate:ADP phosphotransferase 1

C: Polyphosphate:ADP phosphotransferase 1

D: Polyphosphate:ADP phosphotransferase 1

hetero molecules

144 kDa, 4 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)	59.976, 70.563, 89.520
Angle α, β, γ (deg.)	75.63, 85.96, 64.72
Int Tables number	1
Space group name H-M	P1

#1: Protein	Polyphosphate:ADP phosphotransferase 1 / Polyphosphate kinase PPK2 1 Mass: 35370.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: SMc02148 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q92SA6, ATP-polyphosphate phosphotransferase
#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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₆O₅
#4: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.45 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris (pH 7.5), 0.12 M Na-formate, 0.12 M Li-sulfate, and 0.4 M NDSB 211 PH range: 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2013 / Details: double mirror
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.87→100 Å / Num. obs: 98873 / % possible obs: 92.7 % / Redundancy: 2.54 % / CC_1/2: 1 / R_merge(I) obs: 0.038 / R_rim(I) all: 0.048 / Net I/σ(I): 14.14
Reflection shell	Resolution: 1.87→1.98 Å / Redundancy: 2.24 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 12622 / CC_1/2: 0.69 / R_rim(I) all: 0.6 / % possible all: 73.5

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3czq

3czq

Resolution: 1.87→34.321 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 25.28

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2206	1087	1.1 %	RANDOM
R_work	0.1773	-	-	-
obs	0.1778	98865	92.79 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.87→34.321 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9484	0	149	554	10187

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9920
X-RAY DIFFRACTION	f_angle_d	0.82	13395
X-RAY DIFFRACTION	f_dihedral_angle_d	11.798	5882
X-RAY DIFFRACTION	f_chiral_restr	0.051	1348
X-RAY DIFFRACTION	f_plane_restr	0.005	1742

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 (%)
1.8677-1.9527	0.2773	99	0.2719	8872	X-RAY DIFFRACTION	68
1.9527-2.0557	0.2916	139	0.2351	12540	X-RAY DIFFRACTION	95
2.0557-2.1845	0.2523	141	0.2127	12711	X-RAY DIFFRACTION	97
2.1845-2.3531	0.2687	141	0.2046	12640	X-RAY DIFFRACTION	96
2.3531-2.5898	0.2465	142	0.1997	12741	X-RAY DIFFRACTION	97
2.5898-2.9644	0.2605	142	0.198	12799	X-RAY DIFFRACTION	97
2.9644-3.7341	0.2239	142	0.171	12752	X-RAY DIFFRACTION	97
3.7341-34.3269	0.1753	141	0.1465	12723	X-RAY DIFFRACTION	97

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	7.1992	-5.1701	0.2408	9.1286	2.5053	6.5839	-0.2866	-0.5162	0.7599	0.2396	-0.2571	0.3153	-0.2521	-0.3226	0.5413	0.2053	-0.011	-0.0656	0.673	0.07	0.6305	17.6432	25.9763	12.8044
2	5.9823	-1.3979	0.7321	1.5935	-0.5536	1.9938	0.1355	0.6992	0.235	-0.3088	-0.1209	0.226	0.0661	-0.0322	-0.013	0.298	0.0406	-0.0228	0.4405	0.1253	0.3253	44.9715	27.3782	3.8236
3	1.3378	0.5021	0.2923	0.6966	-0.138	2.2491	0.0354	0.0651	0.2716	0.0242	-0.0682	0.0859	-0.0667	-0.1687	0.049	0.1607	0.0414	0.0114	0.2406	0.0381	0.2635	46.9916	27.0352	26.3181
4	0.8377	0.6935	0.92	2.0007	1.0337	1.9397	-0.017	0.0047	0.2614	0.0954	0.0688	0.08	-0.006	-0.5499	0.0435	0.265	0.0746	-0.0213	0.4748	0.0532	0.4779	30.3616	25.9389	17.1962
5	1.1013	0.1078	0.3832	2.4599	0.8664	5.2785	-0.0893	0.1784	0.3008	-0.028	-0.0164	0.0082	-0.1822	0.131	0.1548	0.2083	0.0495	-0.0175	0.2652	0.1593	0.3964	46.8259	33.7676	12.7525
6	0.8198	0.1845	0.3334	3.0106	0.6047	5.1179	-0.0249	0.5119	0.8608	-0.1768	-0.1507	-0.2017	-0.4811	0.0541	0.0775	0.3355	-0.026	-0.0106	0.337	0.1828	0.5225	51.9789	36.7437	8.2029
7	5.0522	-0.3197	-2.4819	1.1878	-0.0522	2.9759	0.1485	0.3812	-0.0395	-0.3149	-0.0758	-0.2049	0.3496	0.3077	-0.0738	0.5289	0.1095	-0.0232	0.4503	-0.0378	0.2732	56.4545	0.2968	1.9756
8	1.0179	0.3235	0.1596	0.567	-0.1198	2.1389	0.1069	0.0589	-0.1483	0.0658	-0.0536	-0.0778	0.6229	0.2277	-0.0613	0.4506	0.0974	-0.0056	0.2701	0.0101	0.2241	57.0466	1.1914	21.9587
9	3.1662	-0.3937	1.9301	6.6523	-5.0113	4.8183	-0.1114	-0.2076	-0.1147	1.7199	0.2552	-0.0355	-0.2392	0.5402	-0.1213	0.6679	0.1424	0.074	0.464	0.0391	0.4122	65.855	11.1969	7.5751
10	3.4754	-0.3707	-0.1416	1.3066	0.1869	1.8019	0.1224	0.1816	-0.4177	-0.0874	-0.0668	0.0103	0.9559	0.0192	0.0054	0.6642	0.0712	-0.0133	0.2758	-0.022	0.2918	51.8376	-7.647	12.5666
11	8.6606	2.3393	-1.4527	6.4654	-3.6798	8.102	0.3083	0.4779	-0.5601	0.0902	-0.1042	0.7583	0.562	-0.5809	-0.3154	0.7137	-0.3811	0.1556	0.8341	-0.0019	0.534	31.385	-1.2909	73.6991
12	5.702	0.2383	-2.0224	0.7736	-0.2844	1.948	0.4256	-1.0542	-0.2958	0.5988	-0.2184	0.3262	0.6167	-0.2802	-0.1556	1.0883	-0.3959	-0.0258	0.7424	0.1568	0.4483	46.5142	-0.7989	78.1422
13	7.544	0.2348	-4.3607	2.2561	0.232	7.8162	0.3173	-0.3804	0.2314	0.4521	-0.0218	-0.1092	0.4147	0.4048	-0.2871	0.5567	-0.0098	-0.133	0.3978	0.0438	0.3701	71.0626	4.6495	63.0996
14	1.026	-0.0196	-0.164	0.7953	0.3093	2.0239	0.1797	-0.1765	-0.1163	0.2092	-0.114	0.0728	0.5881	-0.1276	-0.0439	0.5288	-0.1069	-0.012	0.2897	0.0479	0.2384	51.6876	1.5416	51.633
15	9.0401	6.2244	2.2886	5.2879	3.3694	3.7328	-0.7674	0.6628	-0.2696	-1.6336	0.5853	0.0014	-0.3208	-0.8466	0.11	0.805	-0.1864	0.1186	0.5602	-0.009	0.3929	41.3088	9.7188	65.2629
16	2.4577	1.529	-0.3279	1.896	0.0907	2.5115	0.2495	-0.2158	-0.4492	0.4682	-0.094	-0.1126	1.2795	0.0214	-0.0526	0.863	-0.0783	-0.0879	0.3625	0.0776	0.3767	57.9876	-7.4251	61.1048
17	4.6687	3.9617	1.4728	6.5206	-1.6712	4.6185	-0.449	0.5801	0.0552	-0.4452	0.288	-1.199	-0.4228	0.4709	0.089	0.2876	-0.0816	0.0311	0.8373	-0.1331	0.7046	91.6862	30.1386	57.9628
18	7.9308	-0.2161	-0.0794	2.9511	1.201	1.2856	0.0724	-1.1876	0.3627	0.1274	0.2286	-0.5522	-0.2023	0.8688	-0.253	0.3904	-0.1207	-0.0971	0.6755	0.0048	0.4244	80.5167	30.0596	69.0028
19	1.9438	0.435	1.2755	1.2113	0.2555	3.0931	-0.0165	-0.1926	0.0926	0.1496	-0.0645	0.0417	0.2195	-0.3684	0.0831	0.252	-0.0467	0.0279	0.3427	-0.0323	0.255	54.5027	25.7539	62.2601
20	3.9226	1.0616	1.5672	3.4606	1.0741	4.2545	-0.2557	-0.2413	0.4338	0.1108	0.0185	0.2067	0.315	-0.1854	0.0579	0.2744	-0.0455	0.033	0.3545	0.0133	0.2133	56.517	19.0928	59.5152
21	1.4426	0.0449	0.3098	1.4977	0.3986	3.2681	0.0909	0.1004	0.2054	-0.0644	-0.1191	-0.1373	-0.1395	0.2921	0.048	0.1457	-0.0162	0.0038	0.2309	0.0377	0.2382	62.6719	28.6677	43.1515
22	1.7957	-0.8456	1.4663	3.7416	-1.876	3.0958	0.0538	0.1395	0.0363	-0.0808	-0.0512	-0.1813	0.0732	0.7016	-0.017	0.2326	-0.0705	-0.0183	0.5175	0.0093	0.4082	78.1197	26.5629	55.7212
23	2.967	-0.828	0.0122	1.1069	-1.281	3.9305	-0.1848	-0.1295	0.3035	0.0004	0.0003	-0.0479	-0.189	-0.1596	0.1572	0.2871	-0.0727	-0.0142	0.2637	-0.0796	0.3243	61.5787	34.4837	59.8876
24	5.1902	1.2167	0.5744	5.8861	0.8568	6.1785	0.1301	-0.4737	0.6956	0.2441	-0.3265	0.1686	-0.5577	-0.0353	0.1448	0.3029	-0.0083	0.0264	0.2101	-0.0754	0.2916	56.4238	37.5132	64.3293

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 242 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 243 through 272 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 273 through 300 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 210 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 211 through 225 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 226 through 300 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 13 through 28 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 29 through 56 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 57 through 80 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 81 through 210 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 211 through 229 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 230 through 300 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 13 through 28 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 29 through 56 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 57 through 96 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 97 through 112 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 113 through 198 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 199 through 242 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 243 through 272 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 273 through 300 )

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