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

ID or keywords:

Entry

Database: PDB / ID: 9igq

Title

Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with AppCH2p and polyphosphate

Components

Polyphosphate--nucleotide phosphotransferase

Keywords

TRANSFERASE / Polyphosphate Kinase / PPK2-III / NTP / EbPPK

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: 1.7 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	9igq.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9igq.ent.gz		Display	PDB format
PDBx/mmJSON format	9igq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9igq_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9igq_full_validation.pdf.gz	2.8 MB	Display
Data in XML	9igq_validation.xml.gz	65.8 KB	Display
Data in CIF	9igq_validation.cif.gz	88.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/9igq ftp://data.pdbj.org/pub/pdb/validation_reports/ig/9igq	HTTPS FTP

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Related structure data

Related structure data	9igrC 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
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Polyphosphate--nucleotide phosphotransferase

B: Polyphosphate--nucleotide phosphotransferase

C: Polyphosphate--nucleotide phosphotransferase

D: Polyphosphate--nucleotide phosphotransferase

hetero molecules

152 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)	77.888, 110.734, 152.585
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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	PRO	PRO	A	A	3 - 295	3 - 295
2	1	1	ASN	ASN	PRO	PRO	B	B	3 - 295	3 - 295
3	2	2	ASN	ASN	ASP	ASP	A	A	3 - 289	3 - 289
4	2	2	ASN	ASN	ASP	ASP	C	C	3 - 289	3 - 289
5	3	3	ASN	ASN	TYR	TYR	A	A	3 - 288	3 - 288
6	3	3	ASN	ASN	TYR	TYR	D	D	3 - 288	3 - 288
7	4	4	ASN	ASN	ASP	ASP	B	B	3 - 289	3 - 289
8	4	4	ASN	ASN	ASP	ASP	C	C	3 - 289	3 - 289
9	5	5	ALA	ALA	TYR	TYR	B	B	2 - 288	2 - 288
10	5	5	ALA	ALA	TYR	TYR	D	D	2 - 288	2 - 288
11	6	6	ASN	ASN	TYR	TYR	C	C	3 - 288	3 - 288
12	6	6	ASN	ASN	TYR	TYR	D	D	3 - 288	3 - 288

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 Source: (gene. exp.) Erysipelotrichaceae bacterium (bacteria) Strain: UBA9076 / Gene: DHS57_05705 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
Source: (gene. exp.)

Erysipelotrichaceae bacterium (bacteria)
Strain: UBA9076 / Gene: DHS57_05705
Production host:

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

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Non-polymers , 8 types, 1032 molecules

#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: 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.: 2 / Source method: obtained synthetically / Formula: H₁₃O₃₄P₁₁ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-BEZ / BENZOIC ACID Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₂
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#8: Chemical	ChemComp-A1I4D / bis[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl] hydrogen phosphate Mass: 577.875 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₉O₂₂P₇ / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1008 / 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: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: MPD 20%, sodium acetate 0.1 M, sodium chloride 0.2 M

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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: 1.7→48.9 Å / Num. obs: 145127 / % possible obs: 98.4 % / Redundancy: 13.7 % / B_iso Wilson estimate: 18.53 Å² / CC_1/2: 0.998 / CC star: 0.999 / R_pim(I) all: 0.0533 / R_rim(I) all: 0.193 / Net I/σ(I): 10.76
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.51 / Num. unique obs: 23262 / CC_1/2: 0.635 / CC star: 0.878 / R_pim(I) all: 0.593 / R_rim(I) all: 2.15 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→48.9 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.965 / SU B: 5.289 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1969	7180	4.968 %
R_work	0.1671	137349	-
all	0.169	-	-
obs	-	144529	99.467 %

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: 30.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.228 Å²	0 Å²	0 Å²
2-	-	0.946 Å²	-0 Å²
3-	-	-	-0.717 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→48.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9812	0	330	1008	11150

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	10422
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	9576
X-RAY DIFFRACTION	r_angle_refined_deg	2.211	1.873	14171
X-RAY DIFFRACTION	r_angle_other_deg	0.814	1.805	22104
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.95	5	1181
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.688	5	60
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.161	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.05	10	1886
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.737	10	554
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	1507
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	11952
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2420
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	2043
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.155	0.2	8496
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	5026
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	5524
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	783
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.34	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.214	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	2.396	1.673	4688
X-RAY DIFFRACTION	r_mcbond_other	2.393	1.673	4688
X-RAY DIFFRACTION	r_mcangle_it	3.501	2.993	5863
X-RAY DIFFRACTION	r_mcangle_other	3.501	2.994	5864
X-RAY DIFFRACTION	r_scbond_it	4.704	2.23	5734
X-RAY DIFFRACTION	r_scbond_other	4.703	2.23	5735
X-RAY DIFFRACTION	r_scangle_it	6.936	3.924	8302
X-RAY DIFFRACTION	r_scangle_other	6.935	3.924	8303
X-RAY DIFFRACTION	r_lrange_it	8.355	20.017	12187
X-RAY DIFFRACTION	r_lrange_other	8.336	19.47	11924
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.063	0.05	10017
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	9717
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.086	0.05	9662
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.086	0.05	9677
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.091	0.05	9646
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.077	0.05	9895

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	0.06304	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06304	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08288	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08288	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08554	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08554	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08576	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.08576	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.0913	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.0913	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.07735	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07735	0.05008

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
1.7-1.744	0.295	543	0.292	10038	0.292	10585	0.938	0.941	99.9622	0.275
1.744-1.792	0.276	537	0.258	9822	0.259	10366	0.946	0.952	99.9325	0.24
1.792-1.844	0.264	475	0.24	9607	0.241	10094	0.951	0.959	99.8811	0.219
1.844-1.9	0.27	482	0.232	9281	0.234	9788	0.951	0.964	99.7446	0.205
1.9-1.963	0.319	490	0.278	8909	0.28	9518	0.948	0.96	98.7497	0.246
1.963-2.031	0.352	432	0.298	8480	0.301	9175	0.944	0.959	97.1335	0.251
2.031-2.108	0.31	443	0.271	8252	0.273	8892	0.957	0.966	97.7845	0.216
2.108-2.194	0.256	430	0.213	8047	0.215	8564	0.965	0.976	98.9841	0.166
2.194-2.291	0.206	394	0.166	7838	0.168	8245	0.976	0.984	99.8423	0.133
2.291-2.403	0.186	374	0.137	7472	0.139	7849	0.981	0.989	99.9618	0.114
2.403-2.532	0.175	388	0.13	7097	0.133	7487	0.982	0.99	99.9733	0.111
2.532-2.685	0.178	346	0.13	6783	0.132	7129	0.981	0.99	100	0.115
2.685-2.87	0.173	313	0.137	6371	0.139	6684	0.982	0.989	100	0.124
2.87-3.099	0.162	296	0.129	5953	0.13	6253	0.984	0.99	99.936	0.12
3.099-3.394	0.181	291	0.142	5471	0.144	5765	0.981	0.988	99.948	0.136
3.394-3.792	0.152	245	0.136	4985	0.137	5235	0.985	0.989	99.9045	0.135
3.792-4.374	0.138	233	0.121	4432	0.122	4665	0.989	0.991	100	0.128
4.374-5.347	0.142	212	0.133	3746	0.133	3962	0.989	0.991	99.899	0.145
5.347-7.517	0.207	165	0.166	2965	0.168	3143	0.976	0.984	99.5864	0.181
7.517-48.9	0.191	90	0.194	1763	0.194	1858	0.976	0.973	99.7309	0.222

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	0.4013	0.2541	-0.0116	0.9881	0.2239	0.9443	0.0096	-0.0235	-0.0256	0.0261	-0.0118	0.1163	0.1047	-0.183	0.0022	0.0946	-0.0202	-0.0099	0.0808	0.0328	0.044	11.617	-10.2758	-2.4679
2	0.7002	-0.1325	-0.0245	0.7769	-0.1031	0.8864	0.0136	0.0169	-0.0219	-0.0024	-0.0092	-0.0992	0.0666	0.1277	-0.0045	0.0687	0.0105	0.0016	0.0532	-0.0238	0.0402	28.8051	-8.5455	-34.3005
3	0.4073	-0.2028	0.025	0.781	0.2118	0.9941	0.0269	0.0616	-0.0035	-0.0846	-0.0243	-0.0155	-0.0788	-0.0593	-0.0027	0.0621	0.0067	0.0014	0.0349	0.005	0.0022	17.3047	16.594	-36.1305
4	0.5535	-0.0026	0.1718	0.8168	-0.1626	1.1876	0.0232	-0.0437	-0.0455	0.031	0.0046	0.02	-0.0168	-0.0179	-0.0278	0.0308	0.0033	-0.0023	0.0213	-0.0035	0.0073	19.2031	16.5206	-0.3908

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 404
2	X-RAY DIFFRACTION	2	ALL	B	2 - 403
3	X-RAY DIFFRACTION	3	ALL	C	3 - 404
4	X-RAY DIFFRACTION	4	ALL	D	2 - 403

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