PDB-9grh: Crystal structure of the C-terminal phosphatase domain from Sacch...

ID or keywords:

Entry

Database: PDB / ID: 9grh

Title

Crystal structure of the C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo)

Components

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

Keywords

BIOSYNTHETIC PROTEIN / Inositol pyrophosphate / inositol pyrophosphate phosphatase / histidine acid phosphatase / phytase / enzyme mechanism / GAF domain / phosphate homeostasis

Function / homology

Function and homology information

inositol hexakisphosphate 4-kinase activity / inositol hexakisphosphate 6-kinase activity / inositol hexakisphosphate 3-kinase activity / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 3.2 Å

Authors

Raia, P. / Lee, K. / Hothorn, M.

Funding support

Switzerland,

United States, 2items

Citation

Journal: Nat Commun / Year: 2025
Title: A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.
Authors: Raia, P. / Lee, K. / Bartsch, S.M. / Rico-Resendiz, F. / Portugal-Calisto, D. / Vadas, O. / Panse, V.G. / Fiedler, D. / Hothorn, M.

History

Deposition	Sep 11, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9grh.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9grh.ent.gz	987.5 KB	Display	PDB format
PDBx/mmJSON format	9grh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9grh_validation.pdf.gz	465.8 KB	Display	wwPDB validaton report
Full document	9grh_full_validation.pdf.gz	488.5 KB	Display
Data in XML	9grh_validation.xml.gz	71.7 KB	Display
Data in CIF	9grh_validation.cif.gz	90.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/9grh ftp://data.pdbj.org/pub/pdb/validation_reports/gr/9grh	HTTPS FTP

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Related structure data

Related structure data	9gr8C 9grnC 9groC 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	#225 - Sep 2018 Phytase similarity (4) #257 - May 2021 Fetal Hemoglobin similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

C: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

D: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

hetero molecules

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

1

A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

hetero molecules

defined by author
Evidence: gel filtration
65.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

hetero molecules

defined by author
65.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

hetero molecules

defined by author
65.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

hetero molecules

defined by author
65.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.473, 194.857, 84.441
Angle α, β, γ (deg.)	90.00, 112.16, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase / InsP6 and PP-IP5 kinase Mass: 65788.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VIP1, YLR410W / Cell line (production host): Tnao / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q06685, diphosphoinositol-pentakisphosphate 1-kinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
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: 2.44 Å³/Da / Density % sol: 49.69 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1 M Tris pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999993 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999993 Å / Relative weight: 1
Reflection	Resolution: 3.05→48.71 Å / Num. obs: 48030 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / CC_1/2: 1 / R_rim(I) all: 0.153 / Net I/σ(I): 10.1
Reflection shell	Resolution: 3.05→3.23 Å / Redundancy: 7.2 % / Num. unique obs: 7738 / CC_1/2: 0.482 / R_rim(I) all: 1.714 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 3.2→48.71 Å / SU ML: 1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.276	1981	4.76 %
R_work	0.2183	-	-
obs	0.2249	41655	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.2→48.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15712	0	2	0	15714

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	16042
X-RAY DIFFRACTION	f_angle_d	0.483	21614
X-RAY DIFFRACTION	f_dihedral_angle_d	10.175	6228
X-RAY DIFFRACTION	f_chiral_restr	0.039	2375
X-RAY DIFFRACTION	f_plane_restr	0.003	2757

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 (%)
3.2-3.28	0.3851	142	0.2941	2844	X-RAY DIFFRACTION	95
3.28-3.37	0.3446	148	0.2813	2871	X-RAY DIFFRACTION	95
3.37-3.47	0.3241	140	0.2744	2752	X-RAY DIFFRACTION	95
3.47-3.58	0.3217	144	0.2676	2835	X-RAY DIFFRACTION	95
3.58-3.71	0.3171	141	0.2537	2812	X-RAY DIFFRACTION	95
3.71-3.86	0.3311	145	0.2448	2862	X-RAY DIFFRACTION	95
3.86-4.03	0.2857	143	0.2357	2808	X-RAY DIFFRACTION	95
4.03-4.24	0.2667	141	0.2243	2851	X-RAY DIFFRACTION	95
4.24-4.51	0.2577	136	0.2052	2814	X-RAY DIFFRACTION	95
4.51-4.86	0.2175	140	0.1982	2794	X-RAY DIFFRACTION	95
4.86-5.34	0.2916	142	0.2028	2848	X-RAY DIFFRACTION	95
5.35-6.12	0.2667	141	0.2218	2846	X-RAY DIFFRACTION	95
6.12-7.7	0.2592	138	0.2119	2857	X-RAY DIFFRACTION	95
7.71-48.71	0.2688	140	0.1979	2880	X-RAY DIFFRACTION	95

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	4.1855	0.7676	-0.608	2.09	-1.4573	1.5828	0.1001	-0.3048	0.9303	0.3988	0.3397	1.0357	-0.3863	-0.4466	-0.3939	1.1141	0.0914	0.365	0.9435	-0.0577	0.8974	-14.6269	-12.0742	-0.9569
2	3.2487	0.9356	0.1021	6.3224	-0.4941	2.1924	0.0549	0.4622	-0.0869	-0.1758	-0.0154	0.587	0.3299	-0.3176	-0.1011	0.5446	0.0051	0.0445	0.9073	-0.0925	0.6335	-18.9071	-32.9584	-7.0701
3	4.4458	1.5643	-1.7615	1.5148	0.7619	2.594	0.2784	-0.2295	-0.1387	0.1068	-0.1406	-0.1768	-0.1668	0.3511	-0.1504	0.806	0.0175	0.1021	0.719	0.0085	0.4082	6.1537	-24.128	-9.3728
4	0.1282	-0.4753	-0.0989	1.8141	0.3995	0.206	0.3033	0.2102	0.7875	0.0157	0.0626	-1.0099	-0.6811	-0.2782	-0.3926	1.6126	0.0353	0.4194	1.1033	0.1233	0.3631	12.1456	-13.4197	32.1261
5	4.0553	2.4132	0.7	8.002	1.1112	4.4341	-1.2791	2.1247	-0.6011	1.0393	0.653	-1.0014	1.6438	-0.5641	-0.0522	1.441	-0.019	0.3591	1.1937	0.163	1.2114	30.7435	-14.2409	23.3882
6	4.947	-1.5937	-0.071	2.3452	-0.52	1.9588	0.2701	1.1039	0.5289	-0.1542	-0.4334	-0.689	-0.3458	0.1197	0.1653	1.1542	0.0417	0.3536	0.8571	0.2909	0.7041	2.6349	-12.1859	28.0305
7	3.46	-1.1587	-0.6456	6.5429	0.6332	3.5104	0.1306	-0.7904	0.0261	0.1516	-0.183	-0.1793	0.1813	0.6518	-0.1462	0.4449	-0.0903	-0.0894	1.0879	-0.0358	0.6775	14.5626	-32.9257	37.3426
8	3.3759	-1.3366	-0.0756	1.8106	-0.9972	1.0357	0.1403	0.2156	0.0628	0.0666	-0.2304	-0.2177	-0.4639	-0.371	0.0367	0.8833	-0.007	0.2446	0.7408	-0.0637	0.3736	-5.1086	-26.1488	35.526
9	7.8059	-1.9373	-2.7648	4.1021	2.836	5.7734	0.9173	1.2564	-0.0628	-0.1973	-0.8056	-0.0094	-0.4562	-0.6785	-0.3936	0.7919	0.067	0.1273	0.7017	-0.047	0.5175	-10.7594	-27.0221	31.53
10	2.7764	0.6437	0.1823	2.889	-0.8418	0.7863	-0.3949	0.6176	-0.6301	-1.3352	0.18	-0.5325	0.9043	-1.3201	-0.0524	0.9712	-0.0126	0.0542	1.1569	-0.0936	0.7739	17.3328	11.9438	5.1939
11	0.7435	1.1489	0.1325	4.2985	3.1914	8.1311	-0.096	-0.348	-0.5807	-1.2347	1.2158	-1.3059	0.0844	-0.2293	-0.8473	1.1047	0.0751	0.1182	0.9561	-0.0312	1.2094	26.395	11.065	-7.6384
12	1.4166	1.3552	-2.0351	4.7798	-1.5087	3.8127	-0.2742	0.0675	-0.4171	-0.4276	-0.0772	-0.7049	-0.0125	0.2059	0.3386	0.4247	0.1761	0.0749	0.955	-0.0088	0.5597	15.3281	26.9088	10.1117
13	4.0647	0.2555	0.0877	2.4415	1.7566	4.3507	-0.1464	0.1567	-0.2005	-0.106	-0.0577	-0.0004	0.1818	0.1137	0.2994	0.4699	0.2162	-0.0072	0.6914	0.046	0.6158	0.5731	17.6983	28.4612
14	8.1838	3.9175	-4.744	6.7632	-3.3928	5.574	-0.0713	-1.011	-1.1324	0.2862	-0.453	-0.6232	-0.2733	0.4719	0.4678	0.6035	0.1916	0.0168	1.1563	-0.0044	0.6065	9.2674	25.615	26.5135
15	3.3193	0.0995	-0.4994	2.2513	-1.1656	2.7878	0.0465	-0.2267	-0.6153	0.7828	0.2363	0.2959	-0.0311	0.0591	-0.2571	0.7379	0.0848	-0.0728	0.5676	0.0781	0.7457	35.6806	10.6306	53.7037
16	3.8555	0.1721	1.3145	4.9567	-0.9477	3.9639	-0.144	0.5016	0.0274	-0.842	-0.1599	0.8229	-0.5462	0.1078	0.4278	0.5876	0.0979	0.0174	1.0793	-0.3186	1.0612	41.4452	13.7556	17.9486
17	3.9614	0.7693	2.9563	3.336	-0.4124	3.5859	0.2469	-1.0443	-1.4883	0.0559	-0.3889	0.7185	0.4322	-0.5497	0.4092	0.5155	-0.0136	0.225	0.7905	-0.2539	1.1379	43.3294	7.3827	28.2123
18	4.9852	-3.0616	-0.1329	4.9198	-0.7779	0.5887	-0.4601	-0.8641	0.7903	1.1783	0.0129	-0.506	-0.1817	1.4955	-0.1005	0.68	-0.063	-0.0265	1.5242	0.1155	0.519	51.8711	32.9131	49.4584
19	4.4516	-1.3264	-1.6108	6.2048	0.9901	5.2096	0.2234	0.4296	-0.2736	0.6541	-0.3416	0.7977	-0.1929	-0.1833	0.1303	0.5415	-0.018	0.1425	0.7401	0.0117	0.5196	38.0637	31.8253	46.2933
20	4.6684	1.2223	1.1775	3.0465	-1.0729	3.2033	-0.1595	-0.7223	-0.4296	0.1609	0.1644	-0.1334	-0.1009	-0.1322	-0.0267	0.5628	0.0832	0.0547	0.8834	-0.0656	0.5282	58.7712	15.8776	25.503
21	3.6011	1.1706	-1.9231	3.8765	-1.0668	6.6543	-0.1149	0.1118	0.0446	-0.5665	0.4901	0.0671	0.2254	0.9199	-0.2001	0.4306	0.2374	-0.0111	1.1456	-0.1179	0.6123	55.3289	20.0386	15.3753
22	3.3242	-0.9322	-2.2778	2.987	-0.7508	3.7289	-0.4573	0.3636	-0.228	-0.1177	-0.2696	0.2506	0.3676	-0.7504	0.4635	0.4466	0.0311	-0.0852	1.0544	-0.3072	0.5954	49.7855	25.0382	23.3806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 536 through 721 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 722 through 922 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 923 through 1088 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 535 through 581 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 582 through 616 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 617 through 721 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 722 through 819 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 820 through 1047 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1048 through 1088 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 535 through 581 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 582 through 652 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 653 through 950 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 951 through 1047 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1048 through 1088 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 536 through 652 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 653 through 686 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 687 through 721 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 722 through 782 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 783 through 950 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 951 through 1014 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1015 through 1040 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1041 through 1088 )

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