PDB-3wzz: Crystal structure of PIP4KIIBETA

ID or keywords:

Entry

Database: PDB / ID: 3wzz

Title

Crystal structure of PIP4KIIBETA

Components

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

Keywords

TRANSFERASE /

LIPID KINASE / PHOSPHOINOSITIDE SIGNALING

Function / homology

Function and homology information

1-phosphatidylinositol-5-phosphate 4-kinase /

1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus /

1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Takeuchi, K. / Lo, Y.H. / Sumita, K. / Senda, M. / Terakawa, J. / Dimitoris, A. / Locasale, J.W. / Sasaki, M. / Yoshino, H. / Zhang, Y. ...

Citation

Journal: Mol.Cell / Year: 2016
Title: The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Authors: Sumita, K. / Lo, Y.H. / Takeuchi, K. / Senda, M. / Kofuji, S. / Ikeda, Y. / Terakawa, J. / Sasaki, M. / Yoshino, H. / Majd, N. / Zheng, Y. / Kahoud, E.R. / Yokota, T. / Emerling, B.M. / ...

History

Deposition	Oct 8, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3wzz.cif.gz	277 KB	Display	PDBx/mmCIF format
PDB format	pdb3wzz.ent.gz	225.9 KB	Display	PDB format
PDBx/mmJSON format	3wzz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wz/3wzz ftp://data.pdbj.org/pub/pdb/validation_reports/wz/3wzz	HTTPS FTP

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Related structure data

Related structure data	3x01C 3x02C 3x03C 3x04C 3x05C 3x06C 3x07C 3x08C 3x09C 3x0aC 3x0bC 3x0cC 1bo1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3x03-d 3x08-d 3x07-d 3x0a-d 3x0c-d 3x02-d 3x05-d 3x06-d 3x09-d 3x04-d Search similar-shape structures by Omokage search (details) 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	#134 - Feb 2011 Integrin similarity (6) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

Deposited unit

A: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

B: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	107.137, 182.404, 105.399
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta / 1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / ...1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / Phosphatidylinositol 5-phosphate 4-kinase type II beta / PI(5)P 4-kinase type II beta / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta Mass: 44928.902 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2B / Production host: Escherichia Coli (E. coli) References: UniProt: P78356, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta / 1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / ...

Mass: 44928.902 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PIP4K2B / Production host:

Escherichia Coli (E. coli)
References: UniProt: P78356,

1-phosphatidylinositol-5-phosphate 4-kinase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.07 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE CONTAININ, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 22, 2012
Radiation	Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→69.47 Å / Num. obs: 32017 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / B_iso Wilson estimate: 56.26 Å²
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.414 / Mean I/σ(I) obs: 3.65 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(PHENIX.REFINE: 1.7.3_928)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BO1

1bo1

Resolution: 2.6→52.7 Å / SU ML: 0.47 / σ(F): 1.28 / Phase error: 28.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26	1600	5 %	Randon
R_work	0.211	-	-	-
all	0.285	-	-	-
obs	0.213	32017	99.6 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.3 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso mean: 71.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.1269 Å²	-0 Å²	0 Å²
2-	-	-7.9179 Å²	-0 Å²
3-	-	-	3.791 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→52.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5162	0	0	51	5213

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5286
X-RAY DIFFRACTION	f_angle_d	1.149	7114
X-RAY DIFFRACTION	f_dihedral_angle_d	17.11	2012
X-RAY DIFFRACTION	f_chiral_restr	0.077	777
X-RAY DIFFRACTION	f_plane_restr	0.005	917

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.6001-2.6407	0.4429	141	0.3677	2658	100
2.6407-2.684	0.5042	138	0.3829	2669	100
2.684-2.7303	0.4373	141	0.3153	2634	100
2.7303-2.7799	0.3573	144	0.2771	2674	100
2.7799-2.8334	0.3642	136	0.2836	2612	100
2.8334-2.8912	0.3952	141	0.2681	2648	100
2.8912-2.9541	0.3282	139	0.2702	2669	100
2.9541-3.0228	0.3509	138	0.2453	2632	100
3.0228-3.0983	0.3155	139	0.2347	2659	100
3.0983-3.1821	0.2901	139	0.2363	2665	100
3.1821-3.2757	0.3338	137	0.2311	2635	100
3.2757-3.3814	0.3159	141	0.2253	2632	100
3.3814-3.5023	0.2811	136	0.229	2644	100
3.5023-3.6425	0.2848	146	0.2209	2677	100
3.6425-3.8082	0.2577	137	0.1999	2626	100
3.8082-4.0089	0.2417	140	0.1784	2650	100
4.0089-4.26	0.1896	140	0.1607	2669	100
4.26-4.5887	0.1764	134	0.1508	2645	100
4.5887-5.0502	0.2015	139	0.1444	2657	100
5.0502-5.7802	0.2517	142	0.1729	2642	100
5.7802-7.2793	0.2576	139	0.191	2633	100
7.2793-52.7103	0.1943	130	0.1776	2481	93

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	4.6682	0.7883	1.4471	4.2108	0.561	2.4496	-0.0237	0.0985	0.2065	-0.5161	0.1884	0.1507	-0.1104	0.1879	-0.1046	0.2101	0.0108	0.0803	0.3638	0.011	0.1496	40.7286	37.8417	-12.7338
2	9.7408	1.3828	-0.4754	5.5314	1.189	6.224	-0.3076	-0.5187	0.3643	-0.0479	0.2821	0.7021	0.0242	-0.4531	0.0454	0.3042	0.0363	0.0635	0.4614	-0.1175	0.3265	37.8381	44.3683	-2.9625
3	7.7298	0.5246	-0.2106	5.1546	-0.0983	5.623	-0.204	0.0282	1.1706	-0.289	0.2526	-0.2629	-0.2425	0.5162	-0.0168	0.3347	-0.0702	0.0684	0.278	-0.0906	0.3506	49.6526	50.1773	-8.3203
4	3.9968	0.7164	0.0185	4.3021	2.2515	2.8148	-0.212	-0.3542	1.0476	-0.3613	0.0507	0.1975	-0.4951	0.0651	0.1109	0.331	-0.01	0.0275	0.4201	-0.0956	0.4919	44.9626	56.8029	-5.0209
5	1.0111	1.0395	-1.0264	5.2976	-0.9323	3.0767	0.2312	-0.4735	2.4761	-0.2947	0.2923	0.9324	-0.5584	-0.5033	-0.081	0.555	0.1695	0.1514	0.6941	-0.3915	1.6474	43.4702	72.5693	2.5223
6	7.6179	-0.0402	-0.8322	5.2247	0.7846	9.3977	-0.5261	-0.2017	0.4392	-0.372	0.1069	-0.5603	0.0315	1.2448	0.517	0.3126	-0.1466	0.1035	0.566	-0.1343	0.7658	60.8512	60.0235	0.3187
7	4.0846	-1.4417	-2.2542	0.634	0.3753	2.125	0.1664	-0.7681	0.4532	0.5618	0.3102	0.1207	0.166	-0.2929	-0.0456	0.3904	0.122	0.1707	0.7537	-0.3685	0.9038	31.743	61.7097	13.8579
8	2.4545	-0.6939	-0.8814	1.0688	-0.2167	0.6823	0.3769	-1.6341	0.8783	1.1415	-0.591	-0.4326	-0.6254	-0.3351	-0.1639	0.4489	-0.0803	0.2041	1.1124	-0.5889	0.6395	45.1322	57.5996	15.2812
9	4.454	0.5155	-0.8275	3.162	-0.7018	6.2972	0.276	-0.132	1.8022	0.1329	-0.2701	-0.1267	-0.8078	0.4143	-0.0101	0.409	-0.0679	0.0882	0.5703	-0.177	0.9454	56.3078	65.9998	-0.9558
10	5.4087	1.6584	-0.9578	3.3228	0.6073	3.2902	0.1278	0.2607	-0.0388	-0.4262	0.0159	-0.0431	-0.1749	0.1744	-0.1026	0.2954	0.0241	0.0089	0.2879	0.0204	0.1505	33.7927	24.7927	-17.2051
11	9.2734	1.0678	2.7421	8.0388	-1.4642	5.4911	0.0526	0.0498	-0.7585	0.2218	0.1287	0.0272	0.4411	0.4442	-0.0572	0.3763	0.0326	0.0269	0.2455	0.0377	0.3617	34.9563	11.7347	-14.0698
12	3.0649	-1.4217	-2.9895	6.4555	1.69	2.8827	-0.1148	1.2034	-0.41	-1.1568	-0.1942	1.5101	0.1309	-0.8676	0.1929	0.5989	-0.1182	-0.2277	0.6583	-0.0242	0.5269	17.2741	15.0493	-23.9762
13	3.2674	0.1666	0.7836	4.8688	0.9996	1.0628	-0.2136	0.1598	-0.614	-0.6784	0.2834	0.2596	0.6982	0.1829	-0.0788	0.547	0.0053	-0.0243	0.2959	-0.0585	0.2531	28.9314	4.9127	-21.2276
14	2.876	0.5931	1.1255	1.8093	0.426	4.0445	0.8474	0.6384	-1.1648	-0.3971	-0.0559	-0.2502	0.5322	1.1119	-0.5186	1.1642	0.0822	-0.1514	0.6306	-0.3614	0.9293	30.3541	-12.4929	-24.647
15	5.358	-0.0771	0.9069	6.4096	-0.6983	8.014	-0.309	-0.2129	-0.839	-0.3497	0.6352	1.3395	0.8427	-1.3349	-0.2728	0.6949	-0.1005	-0.1623	0.636	0.0002	0.8825	11.6055	-1.8405	-16.8422
16	3.1059	-0.0491	0.1217	4.6897	0.2478	4.1096	0.4984	0.1574	-0.3724	-0.6032	-0.3012	-0.2617	1.63	0.5712	-0.166	0.8126	0.0551	0.0358	0.2389	-0.0646	0.6016	29.7244	-5.4897	-12.4612
17	4.0889	-0.3284	1.8943	8.0017	1.2924	3.8203	0.2125	-0.2752	-0.7763	0.6436	-0.1613	-0.0778	1.7016	-0.7652	-0.117	0.9461	-0.1094	-0.0802	0.3594	0.0568	0.6228	24.6875	-7.4644	-6.2924
18	2.0547	0.6278	1.8801	0.3477	1.1632	3.8878	0.4846	0.4666	-0.6494	0.0639	-0.3207	0.3236	0.4561	-0.1793	-0.0074	0.7734	-0.0984	-0.146	0.3576	-0.0214	0.4449	22.5328	-1.636	-22.0855
19	3.6134	0.1885	0.4805	4.7124	0.2665	4.6173	0.3493	0.2328	-0.3828	-1.4061	0.0379	1.2249	1.0862	-0.8928	-0.1618	1.0732	-0.2317	-0.2786	0.6826	-0.197	0.9389	13.8101	-7.2328	-25.6376

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 32:110)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 111:138)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 139:174)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 175:227)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 228:253)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 254:279)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 280:304)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 305:360)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 361:416)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 32:109)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 110:153)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 154:173)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 174:227)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 228:253)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 254:273)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 274:341)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESSEQ 342:360)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 361:399)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESSEQ 400:416)

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