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- PDB-9gia: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bac... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9gia

Title

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form

Components

Polyphosphate-AMP phosphotransferase

Keywords

TRANSFERASE / Polyphosphate kinase 2 (PPK2) / phosphotransferase / enzyme structure / kinase / polyphosphate.

Function / homology

Transferases / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / polyphosphate kinase activity / P-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / PYROPHOSPHATE 2- / Polyphosphate-AMP phosphotransferase

Function and homology information

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Saleem-Batcha, R. / Keppler, M. / Kuge, M. / Andexer, J.N.

Funding support

Germany, European Union, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form
Authors: Saleem-Batcha, R. / Keppler, M. / Kuge, M. / Andexer, J.N.

History

Deposition	Aug 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9gia.cif.gz	124.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9gia.ent.gz	94.4 KB	Display	PDB format
PDBx/mmJSON format	9gia.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gia_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9gia_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9gia_validation.xml.gz	22.9 KB	Display
Data in CIF	9gia_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/9gia ftp://data.pdbj.org/pub/pdb/validation_reports/gi/9gia	HTTPS FTP

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Related structure data

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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

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Assembly

Deposited unit

A: Polyphosphate-AMP phosphotransferase

B: Polyphosphate-AMP phosphotransferase

hetero molecules

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

1

A: Polyphosphate-AMP phosphotransferase

hetero molecules

A: Polyphosphate-AMP phosphotransferase

hetero molecules

A: Polyphosphate-AMP phosphotransferase

hetero molecules

A: Polyphosphate-AMP phosphotransferase

hetero molecules

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

2

B: Polyphosphate-AMP phosphotransferase

hetero molecules

B: Polyphosphate-AMP phosphotransferase

hetero molecules

B: Polyphosphate-AMP phosphotransferase

hetero molecules

B: Polyphosphate-AMP phosphotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.134, 116.815, 130.540
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-417- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 19 - 269 / Label seq-ID: 19 - 269

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein	Polyphosphate-AMP phosphotransferase / UDP-galactose-lipid carrier transferase Mass: 34477.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: pap, BC_1755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81F46, Transferases
#2: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.93 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 2000 or 4000 , Tris buffer pH 8.5 and Li2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2020 / Details: Two-stage focusing X-ray optics
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.42→48.604 Å / Num. obs: 26950 / % possible obs: 98.6 % / Redundancy: 6.4 % / CC_1/2: 0.99 / R_merge(I) obs: 0.11 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.42→2.52 Å / R_merge(I) obs: 1.07 / Num. unique obs: 10904 / CC_1/2: 0.53

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
AutoProcess		data processing
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→48.604 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.911 / SU B: 13.028 / SU ML: 0.266 / Cross valid method: FREE R-VALUE / ESU R: 0.522 / ESU R Free: 0.314
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1177	5 %	RANDOM
R_work	0.21	22363	-	-
all	0.213	-	-	-
obs	-	23540	99.733 %	-

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: 62.603 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.008 Å²	-0 Å²	0 Å²
2-	-	-0.035 Å²	-0 Å²
3-	-	-	0.027 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→48.604 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4288	0	48	58	4394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4440
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4192
X-RAY DIFFRACTION	r_angle_refined_deg	1.678	1.868	5972
X-RAY DIFFRACTION	r_angle_other_deg	0.587	1.82	9680
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.752	5	500
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.141	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.311	10	856
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.048	10	232
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	602
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5140
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1060
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	887
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	3732
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	2042
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2244
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	69
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.144	0.2	37
X-RAY DIFFRACTION	r_nbd_other	0.131	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.194	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.068	5.91	2006
X-RAY DIFFRACTION	r_mcbond_other	6.068	5.911	2006
X-RAY DIFFRACTION	r_mcangle_it	8.62	10.629	2504
X-RAY DIFFRACTION	r_mcangle_other	8.619	10.632	2505
X-RAY DIFFRACTION	r_scbond_it	7.249	6.6	2434
X-RAY DIFFRACTION	r_scbond_other	7.156	6.567	2414
X-RAY DIFFRACTION	r_scangle_it	10.716	11.803	3468
X-RAY DIFFRACTION	r_scangle_other	10.66	11.733	3438
X-RAY DIFFRACTION	r_lrange_it	12.893	56.892	4923
X-RAY DIFFRACTION	r_lrange_other	12.896	56.894	4920
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.112	0.05	8372

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	0.1117	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.1117	0.05008

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 (%)
2.55-2.616	0.408	86	0.408	1639	X-RAY DIFFRACTION	99.5384
2.616-2.687	0.531	82	0.41	1571	X-RAY DIFFRACTION	99.6984
2.687-2.765	0.423	82	0.345	1548	X-RAY DIFFRACTION	99.8775
2.765-2.85	0.386	78	0.311	1486	X-RAY DIFFRACTION	99.8723
2.85-2.943	0.301	77	0.23	1450	X-RAY DIFFRACTION	99.9346
2.943-3.046	0.307	74	0.225	1422	X-RAY DIFFRACTION	99.9332
3.046-3.16	0.305	72	0.227	1362	X-RAY DIFFRACTION	99.8607
3.16-3.289	0.306	69	0.227	1317	X-RAY DIFFRACTION	99.8559
3.289-3.434	0.249	67	0.233	1274	X-RAY DIFFRACTION	99.2598
3.434-3.601	0.295	63	0.224	1188	X-RAY DIFFRACTION	99.7608
3.601-3.795	0.226	61	0.198	1158	X-RAY DIFFRACTION	100
3.795-4.023	0.285	58	0.184	1111	X-RAY DIFFRACTION	100
4.023-4.299	0.253	54	0.173	1026	X-RAY DIFFRACTION	99.9075
4.299-4.64	0.229	50	0.151	951	X-RAY DIFFRACTION	99.8006
4.64-5.079	0.189	47	0.138	892	X-RAY DIFFRACTION	99.1552
5.079-5.67	0.197	43	0.145	818	X-RAY DIFFRACTION	99.884
5.67-6.533	0.212	38	0.211	723	X-RAY DIFFRACTION	99.8688
6.533-7.965	0.276	33	0.222	624	X-RAY DIFFRACTION	100
7.965-11.116	0.27	26	0.161	493	X-RAY DIFFRACTION	98.2955
11.116-48.604	0.332	17	0.302	310	X-RAY DIFFRACTION	100

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