PDB-6aqe: Crystal structure of PPK2 in complex with Mg ATP

ID or keywords:

Entry

Database: PDB / ID: 6aqe

Title

Crystal structure of PPK2 in complex with Mg ATP

Components

molecule A

Keywords

TRANSFERASE / PPK2 / Kinase / Mg / ATP

Function / homology

Function and homology information

polyphosphate kinase activity / polyphosphate metabolic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.805 Å

Authors

Nocek, B. / Joachimiak, A. / Yakunin, A.

Citation

Journal: Acs Catalysis / Year: 2018
Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases
Authors: Nocek, B.P. / Khusnutdinova, A.N. / Ruszkowski, M. / Flick, R. / Burda, M. / Batyrova, K. / Brown, G. / Mucha, A. / Joachimiak, A. / Berlicki, L. / Yakunin, A.F.

History

Deposition	Aug 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6aqe.cif.gz	246.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6aqe.ent.gz	197.8 KB	Display	PDB format
PDBx/mmJSON format	6aqe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/6aqe ftp://data.pdbj.org/pub/pdb/validation_reports/aq/6aqe	HTTPS FTP

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Related structure data

Related structure data	6an9C 6angC 6anhC 6aqnC 6au0C 6b18C 3rhfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4lal-1 4lal-2 4qrn-2 6qla-d 4fha-d 5usd-1 3bwb-d 4e5s-2 6zl7-d 6jqx-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: molecule A

B: molecule A

hetero molecules

64 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, homotetramer

Unit cell

Length a, b, c (Å)	88.376, 88.376, 190.016
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-830- HOH
2	1	B-799- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	molecule A Mass: 30549.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_0132 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9RY20

#1: Protein

molecule A

Mass: 30549.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0132
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9RY20

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Non-polymers , 6 types, 548 molecules

#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 532 / 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: 3.04 Å³/Da / Density % sol: 59.49 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M CaCl2 0.1 M BisTris 45% MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.81→39.5 Å / Num. obs: 69957 / % possible obs: 100 % / Redundancy: 12.4 % / R_merge(I) obs: 0.1 / Net I/σ(I): 22
Reflection shell	Resolution: 1.81→1.84 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2363: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RHF

3rhf

Resolution: 1.805→39.523 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1864	3510	5.04 %
R_work	0.1615	-	-
obs	0.1628	69615	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.805→39.523 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4307	0	175	532	5014

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	4638
X-RAY DIFFRACTION	f_angle_d	1.618	6313
X-RAY DIFFRACTION	f_dihedral_angle_d	18.116	2783
X-RAY DIFFRACTION	f_chiral_restr	0.103	659
X-RAY DIFFRACTION	f_plane_restr	0.009	798

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 (%)
1.8045-1.8292	0.2497	128	0.2221	2495	X-RAY DIFFRACTION	97
1.8292-1.8554	0.23	140	0.2138	2593	X-RAY DIFFRACTION	100
1.8554-1.8831	0.2891	123	0.2088	2640	X-RAY DIFFRACTION	100
1.8831-1.9125	0.2441	149	0.1961	2606	X-RAY DIFFRACTION	100
1.9125-1.9438	0.2504	157	0.2003	2589	X-RAY DIFFRACTION	100
1.9438-1.9774	0.2295	150	0.1869	2622	X-RAY DIFFRACTION	100
1.9774-2.0133	0.2036	157	0.178	2621	X-RAY DIFFRACTION	100
2.0133-2.052	0.2151	142	0.175	2596	X-RAY DIFFRACTION	100
2.052-2.0939	0.2282	133	0.1774	2609	X-RAY DIFFRACTION	100
2.0939-2.1395	0.2057	166	0.175	2590	X-RAY DIFFRACTION	100
2.1395-2.1892	0.1829	118	0.1666	2621	X-RAY DIFFRACTION	100
2.1892-2.244	0.2182	146	0.1665	2621	X-RAY DIFFRACTION	99
2.244-2.3046	0.2215	127	0.1702	2633	X-RAY DIFFRACTION	99
2.3046-2.3724	0.1776	137	0.163	2585	X-RAY DIFFRACTION	99
2.3724-2.449	0.2014	154	0.1636	2658	X-RAY DIFFRACTION	99
2.449-2.5365	0.2034	134	0.1736	2609	X-RAY DIFFRACTION	99
2.5365-2.6381	0.208	125	0.1715	2650	X-RAY DIFFRACTION	99
2.6381-2.7581	0.208	147	0.1625	2643	X-RAY DIFFRACTION	99
2.7581-2.9035	0.1778	128	0.1553	2659	X-RAY DIFFRACTION	100
2.9035-3.0853	0.1592	131	0.1456	2670	X-RAY DIFFRACTION	100
3.0853-3.3234	0.1708	129	0.144	2679	X-RAY DIFFRACTION	100
3.3234-3.6576	0.1604	144	0.1376	2708	X-RAY DIFFRACTION	100
3.6576-4.1864	0.1503	163	0.1308	2704	X-RAY DIFFRACTION	100
4.1864-5.2724	0.1363	135	0.1449	2774	X-RAY DIFFRACTION	100
5.2724-39.5324	0.2237	147	0.1959	2930	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	1.1142	-0.824	-1.5784	1.2216	1.3539	2.2116	0.0141	0.1334	-0.0055	-0.1418	-0.0423	0.2907	0.0563	-0.4439	0.0274	0.2382	-0.006	-0.0239	0.2903	-0.0086	0.2806	51.191	66.8364	4.724
2	6.9651	-2.5835	-5.6906	4.2785	5.111	8.1494	-0.3095	-0.2898	-0.4364	0.3683	0.0371	0.4187	0.2995	0.0773	0.2601	0.2462	0.0129	-0.0269	0.2035	0.087	0.1915	62.0283	51.8893	18.1844
3	1.779	-1.5188	-0.5771	7.9397	1.1349	1.9942	-0.0286	-0.1469	0.0322	-0.0028	0.1033	0.0731	-0.0175	0.1074	-0.1033	0.106	0.0015	-0.0026	0.2171	0.0237	0.18	67.8121	62.9876	9.0185
4	0.7176	0.297	-0.5833	1.0481	-0.8424	1.4381	-0.0086	-0.078	0.0103	0.0834	-0.0133	-0.0526	-0.1312	0.1114	0.0007	0.1894	-0.0007	-0.0206	0.1896	-0.0105	0.1793	74.9618	65.3781	0.7253
5	1.8267	-1.1398	0.3197	3.0609	-1.631	1.3086	0.0727	0.186	0.0246	-0.3572	-0.0281	0.2387	0.0375	-0.1122	-0.0399	0.2024	0.0067	-0.0151	0.2201	-0.0239	0.1595	67.8387	62.6904	-10.6727
6	0.632	-0.0724	0.1736	1.4728	0.9345	1.6611	-0.0366	-0.0373	0.1321	-0.0693	0.028	-0.0265	-0.2113	0.0087	0.0426	0.1974	0.0111	0.0252	0.2077	0.009	0.2081	65.2305	77.1764	8.0557
7	0.8981	-0.6785	-0.4487	2.1162	0.7873	2.0942	0.0011	-0.075	-0.0609	0.0758	0.0958	0.0285	0.0877	-0.143	0.0048	0.1462	-0.0022	-0.0032	0.2059	0.01	0.2089	58.4101	60.4422	9.3548
8	3.3227	-3.6127	3.6533	3.8618	-3.8035	3.7467	1.0855	0.0524	-0.9024	-0.9772	-0.2862	0.3439	1.39	0.2945	-0.6548	0.5164	0.033	-0.1607	0.3319	0.0785	0.5666	73.4221	30.1581	16.2641
9	0.8283	-0.3917	0.1367	2.1134	-0.7699	0.8474	-0.0518	-0.2505	0.0256	0.2673	0.0817	0.1043	-0.1044	-0.1689	-0.0274	0.2777	0.0048	-0.0049	0.304	-0.0202	0.2131	86.2819	57.4557	34.1968
10	0.847	-0.1581	-0.3141	0.8895	0.2334	1.1142	0.0236	0.052	-0.0058	-0.0538	-0.0202	0.0818	-0.0209	-0.1906	0.015	0.1812	-0.0033	-0.0327	0.2054	0.0042	0.1962	87.6743	54.9421	15.3299
11	1.5731	0.7657	-0.3608	5.4621	-0.4907	1.2691	0.0151	0.0068	-0.1658	-0.0225	-0.0918	-0.3025	0.1704	0.0334	0.0609	0.1935	-0.0071	-0.0227	0.2192	0.004	0.1588	101.5217	48.6602	16.7399
12	1.158	-0.3042	0.3681	0.2297	-0.266	0.6635	-0.011	-0.097	-0.0543	-0.0145	0.0249	0.0316	0.0113	-0.0876	-0.0355	0.1982	-0.0053	0.0065	0.2289	0.0136	0.1741	85.6956	52.0229	25.8838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 76 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 77 through 138 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 139 through 159 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 160 through 216 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 217 through 249 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 250 through 266 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 53 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 121 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 122 through 159 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 160 through 266 )

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