PDB-9igr: Crystal structure of PPK2 class III from Erysipelotrichaceae bact...

ID or keywords:

Entry

Database: PDB / ID: 9igr

Title

Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with polyphosphate

Components

Polyphosphate--nucleotide phosphotransferase

Keywords

TRANSFERASE / Polyphosphate Kinase / PPK2-III / NTP Transferase

Function / homology

Function and homology information

polyphosphate kinase activity / polyphosphate metabolic process
Similarity search - Function

Biological species

Erysipelotrichaceae bacterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.311 Å

Authors

Rasche, R. / Lawrence-Doerner, A.-M. / Cornelissen, N.V. / Kuemmel, D.

Funding support

1items

Citation

Journal: Rsc Chem Biol / Year: 2025
Title: Structure-guided engineering of a polyphosphate kinase 2 class III from an Erysipelotrichaceae bacterium to produce base-modified purine nucleotides
Authors: Mitton-Fry, R.M. / Rasche, R. / Lawrence-Dorner, A.M. / Eschenbach, J. / Tekath, A. / Rentmeister, A. / Kummel, D. / Cornelissen, N.V.

History

Deposition	Feb 20, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9igr.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9igr.ent.gz	814.5 KB	Display	PDB format
PDBx/mmJSON format	9igr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9igr_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9igr_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9igr_validation.xml.gz	54.6 KB	Display
Data in CIF	9igr_validation.cif.gz	69.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/9igr ftp://data.pdbj.org/pub/pdb/validation_reports/ig/9igr	HTTPS FTP

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Related structure data

Related structure data	9igqC C: citing same article (ref.)
Similar structure data	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: Polyphosphate--nucleotide phosphotransferase

B: Polyphosphate--nucleotide phosphotransferase

C: Polyphosphate--nucleotide phosphotransferase

D: Polyphosphate--nucleotide phosphotransferase

hetero molecules

151 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	160.471, 88.265, 125.344
Angle α, β, γ (deg.)	90, 101.151, 90
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
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:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ASN	ASN	THR	THR	A	A	3 - 292	3 - 292
2	1	1	ASN	ASN	THR	THR	B	B	3 - 292	3 - 292
3	2	2	ASN	ASN	THR	THR	A	A	3 - 292	3 - 292
4	2	2	ASN	ASN	THR	THR	C	C	3 - 292	3 - 292
5	3	3	ASN	ASN	THR	THR	A	A	3 - 292	3 - 292
6	3	3	ASN	ASN	THR	THR	D	D	3 - 292	3 - 292
7	4	4	ALA	ALA	HIS	HIS	B	B	2 - 301	2 - 301
8	4	4	ALA	ALA	HIS	HIS	C	C	2 - 301	2 - 301
9	5	5	ASN	ASN	LYS	LYS	B	B	3 - 298	3 - 298
10	5	5	ASN	ASN	LYS	LYS	D	D	3 - 298	3 - 298
11	6	6	ASN	ASN	LYS	LYS	C	C	3 - 298	3 - 298
12	6	6	ASN	ASN	LYS	LYS	D	D	3 - 298	3 - 298

NCS ensembles :

ID	Details
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Polyphosphate--nucleotide phosphotransferase Mass: 36625.246 Da / Num. of mol.: 4 / Mutation: I2A Source method: isolated from a genetically manipulated source Details: C-terminal 6xHis tag Source: (gene. exp.) Erysipelotrichaceae bacterium (bacteria) Strain: UBA9076 / Gene: DHS57_05705 / Plasmid: pET28a(+)_EbPPK2_6H Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A3D5XRJ5

#1: Protein

Polyphosphate--nucleotide phosphotransferase

Mass: 36625.246 Da / Num. of mol.: 4 / Mutation: I2A
Source method: isolated from a genetically manipulated source
Details: C-terminal 6xHis tag
Source: (gene. exp.)

Erysipelotrichaceae bacterium (bacteria)
Strain: UBA9076 / Gene: DHS57_05705 / Plasmid: pET28a(+)_EbPPK2_6H
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3D5XRJ5

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Non-polymers , 5 types, 197 molecules

#2: Chemical	ChemComp-6YY / bis[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate Mass: 897.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₁₃O₃₄P₁₁ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BEZ / BENZOIC ACID Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.98 Å³/Da / Density % sol: 58.73 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: MPD 10 %; NaOAc 0.1 M;NaCl 0.2 M; pH 5.40

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.31→45.11 Å / Num. obs: 72761 / % possible obs: 96.6 % / Redundancy: 6.81 % / B_iso Wilson estimate: 50.64 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_pim(I) all: 0.0525 / R_rim(I) all: 0.137 / Net I/σ(I): 9.03
Reflection shell	Resolution: 2.31→2.45 Å / Redundancy: 7.06 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 11484 / CC_1/2: 0.773 / CC star: 0.934 / R_pim(I) all: 6.53 / R_rim(I) all: 17.36 / % possible all: 94.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
MxCuBE		data collection
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.311→45.109 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.958 / SU B: 17.967 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2127	3729	5.131 %
R_work	0.176	68940	-
all	0.178	-	-
obs	-	72669	96.459 %

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: 67.877 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.021 Å²	0 Å²	3.467 Å²
2-	-	0.562 Å²	0 Å²
3-	-	-	-0.842 Å²

Refinement step

Cycle: LAST / Resolution: 2.311→45.109 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10038	0	215	186	10439

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.012	10472
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9641
X-RAY DIFFRACTION	r_angle_refined_deg	2.747	1.876	14206
X-RAY DIFFRACTION	r_angle_other_deg	0.804	1.807	22260
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.434	5	1187
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.925	5	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.553	10	1920
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.607	10	561
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	1508
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	12021
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2423
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	1991
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	8463
X-RAY DIFFRACTION	r_nbtor_refined	0.196	0.2	5145
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	5875
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	205
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.279	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.108	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	5.641	4.481	4760
X-RAY DIFFRACTION	r_mcbond_other	5.641	4.482	4761
X-RAY DIFFRACTION	r_mcangle_it	7.322	8.05	5943
X-RAY DIFFRACTION	r_mcangle_other	7.325	8.051	5944
X-RAY DIFFRACTION	r_scbond_it	7.962	5.061	5712
X-RAY DIFFRACTION	r_scbond_other	7.646	5.046	5657
X-RAY DIFFRACTION	r_scangle_it	10.083	9.017	8263
X-RAY DIFFRACTION	r_scangle_other	10.025	8.987	8170
X-RAY DIFFRACTION	r_lrange_it	10.683	42.794	11577
X-RAY DIFFRACTION	r_lrange_other	10.609	42.54	11532
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.085	0.05	9612
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.086	0.05	9590
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.082	0.05	9608
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.079	0.05	9929
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.088	0.05	9720
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.085	0.05	9781

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	0.08535	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08535	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08558	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08558	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08205	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08205	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.07894	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.07894	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08842	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08842	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.08539	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08539	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
2.311-2.371	0.338	254	0.323	4734	0.324	5535	0.905	0.92	90.1174	0.311
2.371-2.436	0.364	268	0.333	4879	0.335	5353	0.909	0.927	96.1517	0.323
2.436-2.506	0.323	287	0.276	4937	0.278	5256	0.939	0.951	99.3912	0.256
2.506-2.583	0.275	237	0.247	4874	0.248	5122	0.954	0.959	99.7852	0.225
2.583-2.668	0.293	255	0.26	4667	0.261	4931	0.938	0.945	99.8175	0.237
2.668-2.761	0.304	236	0.242	4522	0.245	4775	0.9	0.951	99.644	0.216
2.761-2.865	0.246	242	0.187	4390	0.19	4653	0.963	0.978	99.5487	0.163
2.865-2.981	0.243	234	0.177	4149	0.18	4411	0.964	0.98	99.3652	0.159
2.981-3.113	0.229	220	0.175	4031	0.178	4252	0.962	0.982	99.9765	0.162
3.113-3.264	0.227	221	0.178	3896	0.18	4120	0.967	0.981	99.9272	0.167
3.264-3.44	0.225	182	0.185	3666	0.187	3851	0.967	0.979	99.9221	0.176
3.44-3.647	0.215	189	0.178	3353	0.18	3711	0.97	0.981	95.446	0.17
3.647-3.897	0.202	111	0.166	2200	0.168	3430	0.977	0.983	67.3761	0.164
3.897-4.207	0.183	137	0.136	2733	0.138	3248	0.982	0.989	88.3621	0.141
4.207-4.604	0.174	133	0.132	2806	0.134	2979	0.984	0.99	98.6573	0.142
4.604-5.141	0.15	161	0.121	2526	0.123	2693	0.988	0.993	99.7772	0.136
5.141-5.924	0.173	132	0.133	2274	0.135	2412	0.984	0.991	99.7512	0.147
5.924-7.224	0.214	111	0.155	1909	0.158	2030	0.976	0.988	99.5074	0.174
7.224-10.088	0.15	74	0.125	1509	0.126	1616	0.988	0.991	97.9579	0.15
10.088-45.109	0.188	45	0.238	885	0.236	948	0.975	0.96	98.1013	0.295

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	1.3077	0.1228	-0.4376	1.2539	-0.1607	1.2942	0.0888	-0.265	0.0465	0.1308	-0.0996	-0.1468	-0.0662	0.2495	0.0108	0.0506	-0.0606	-0.0087	0.122	0.0363	0.1511	47.5986	13.6486	31.1517
2	1.0413	0.1523	-0.1525	1.2959	0.7472	1.3141	0.0917	-0.2193	0.1561	0.05	-0.1416	0.145	-0.1371	-0.1921	0.0499	0.039	0.0143	0.0379	0.1106	-0.0057	0.1367	11.6685	7.2739	30.028
3	0.8823	0.4765	-0.2205	1.5987	-0.598	1.2397	0.0828	-0.3917	-0.1933	0.2923	-0.0924	-0.267	0.0823	0.2524	0.0096	0.1038	-0.0101	-0.1219	0.2976	0.1798	0.2871	50.1563	-11.4556	40.1774
4	1.0928	-0.2024	-0.1625	0.9817	0.4062	1.7219	0.0097	-0.089	-0.1794	0.0932	-0.1157	-0.0192	0.068	-0.1382	0.106	0.0108	-0.0189	-0.0118	0.0471	0.0529	0.1314	17.7675	-17.5731	24.2104

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 401
2	X-RAY DIFFRACTION	2	ALL	B	2 - 402
3	X-RAY DIFFRACTION	3	ALL	C	2 - 402
4	X-RAY DIFFRACTION	4	ALL	D	3 - 401

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