PDB-26ee: Rhodobacter sp. 140A Polyphosphate kinase mutant-D114K/D210S

ID or keywords:

Entry

Database: PDB / ID: 26ee

Title

Rhodobacter sp. 140A Polyphosphate kinase mutant-D114K/D210S

Components

polyphosphate kinase

Keywords

TRANSFERASE / PPK / Tetramer

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Rhodobacter sp. 140A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Li, Z. / Li, Z.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Crystal structure of the D114K/D210S variant of polyphosphate kinase from Rhodobacter sp. 140A.
Authors: Li, Z. / Li, Z.

History

Deposition	Apr 28, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 13, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	26ee.cif.gz	245.8 KB	Display	PDBx/mmCIF format
PDB format	pdb26ee.ent.gz	192.4 KB	Display	PDB format
PDBx/mmJSON format	26ee.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/6e/26ee ftp://data.pdbj.org/pub/pdb/validation_reports/6e/26ee	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: polyphosphate kinase

B: polyphosphate kinase

C: polyphosphate kinase

D: polyphosphate kinase

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
Evidence: The biological assembly is a homotetramer composed of chains A, B, C and D.

Unit cell

Length a, b, c (Å)	58.300, 65.450, 90.360
Angle α, β, γ (deg.)	104.502, 101.044, 100.824
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

End auth comp-ID: ILE / End label comp-ID: ILE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	A	A	25 - 309	25 - 309
2	1	1	GLY	GLY	B	B	25 - 309	25 - 309
3	2	2	ILE	ILE	A	A	26 - 309	26 - 309
4	2	2	ILE	ILE	C	C	26 - 309	26 - 309
5	3	3	GLY	GLY	A	A	25 - 309	25 - 309
6	3	3	GLY	GLY	D	D	25 - 309	25 - 309
7	4	4	ILE	ILE	B	B	26 - 309	26 - 309
8	4	4	ILE	ILE	C	C	26 - 309	26 - 309
9	5	5	GLY	GLY	B	B	25 - 309	25 - 309
10	5	5	GLY	GLY	D	D	25 - 309	25 - 309
11	6	6	ILE	ILE	C	C	26 - 309	26 - 309
12	6	6	ILE	ILE	D	D	26 - 309	26 - 309

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	polyphosphate kinase Mass: 35631.066 Da / Num. of mol.: 4 / Mutation: D114K, D210S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sp. 140A (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5, 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2026
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.43→61.459 Å / Num. obs: 44219 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.065 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.43→2.49 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.79 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3248 / CC_1/2: 0.564 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
Aimless	0.7.7	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→61.459 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.905 / SU B: 0.277 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R: 0.822 / ESU R Free: 0.317
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2669	2133	4.824 %
R_work	0.2203	42084	-
all	0.222	-	-
obs	-	44217	95.489 %

Solvent computation

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

Displacement parameters

B_iso mean: 57.822 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.186 Å²	0.167 Å²	1.51 Å²
2-	-	-0.873 Å²	-0.346 Å²
3-	-	-	-1.415 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→61.459 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9326	0	20	107	9453

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	9530
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9332
X-RAY DIFFRACTION	r_angle_refined_deg	1.054	1.846	12853
X-RAY DIFFRACTION	r_angle_other_deg	0.389	1.801	21432
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.248	5	1142
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.464	5	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.578	10	1779
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.523	10	454
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1390
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11344
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2280
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1934
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	8197
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	4676
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	4904
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	230
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.071	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.27	0.2	30
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.274	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	3.276	5.548	4580
X-RAY DIFFRACTION	r_mcbond_other	3.273	5.547	4579
X-RAY DIFFRACTION	r_mcangle_it	5.133	9.972	5718
X-RAY DIFFRACTION	r_mcangle_other	5.133	9.973	5719
X-RAY DIFFRACTION	r_scbond_it	3.765	6.07	4950
X-RAY DIFFRACTION	r_scbond_other	3.754	6.07	4934
X-RAY DIFFRACTION	r_scangle_it	6.271	10.944	7135
X-RAY DIFFRACTION	r_scangle_other	6.265	10.944	7112
X-RAY DIFFRACTION	r_lrange_it	8.779	57.47	10825
X-RAY DIFFRACTION	r_lrange_other	8.777	57.481	10817
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	9530
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.069	0.05	9568
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.084	0.05	9533
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.077	0.05	9490
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.084	0.05	9442
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.076	0.05	9549

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07527	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07527	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06946	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.06946	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08446	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08446	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.07687	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.07687	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08441	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08441	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.07646	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07646	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.43-2.493	0.349	162	0.338	3081	0.339	3399	0.925	0.923	95.4104	0.313
2.493-2.561	0.348	148	0.313	3055	0.314	3337	0.928	0.935	95.9844	0.286
2.561-2.635	0.418	159	0.322	2985	0.326	3278	0.907	0.938	95.9121	0.291
2.635-2.716	0.339	151	0.292	2850	0.294	3138	0.934	0.949	95.6342	0.254
2.716-2.805	0.337	124	0.283	2780	0.285	3031	0.933	0.952	95.81	0.249
2.805-2.903	0.324	140	0.275	2701	0.278	2964	0.941	0.954	95.8502	0.241
2.903-3.013	0.282	133	0.258	2585	0.26	2830	0.944	0.958	96.0424	0.226
3.013-3.135	0.331	135	0.251	2525	0.255	2771	0.944	0.962	95.9942	0.223
3.135-3.275	0.288	119	0.241	2406	0.243	2648	0.951	0.965	95.355	0.215
3.275-3.434	0.276	125	0.23	2265	0.232	2508	0.956	0.97	95.2951	0.213
3.434-3.619	0.246	126	0.225	2180	0.226	2404	0.962	0.974	95.9235	0.212
3.619-3.838	0.234	102	0.208	2040	0.209	2234	0.971	0.978	95.8818	0.2
3.838-4.102	0.206	102	0.195	1933	0.196	2137	0.976	0.98	95.227	0.191
4.102-4.428	0.209	76	0.174	1822	0.176	1982	0.977	0.983	95.7619	0.174
4.428-4.849	0.221	76	0.159	1666	0.162	1812	0.972	0.985	96.1369	0.164
4.849-5.417	0.287	71	0.175	1511	0.179	1651	0.955	0.982	95.8207	0.179
5.417-6.247	0.228	65	0.212	1296	0.213	1437	0.971	0.976	94.7112	0.211
6.247-7.631	0.24	50	0.196	1136	0.198	1244	0.966	0.979	95.3376	0.204
7.631-10.709	0.161	42	0.133	846	0.135	961	0.982	0.99	92.4037	0.154
10.709-61.459	0.474	27	0.335	421	0.343	539	0.856	0.943	83.1169	0.389

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