PDB-5okm: Crystal structure of human SHIP2 Phosphatase-C2

ID or keywords:

Entry

Database: PDB / ID: 5okm

Title

Crystal structure of human SHIP2 Phosphatase-C2

Components

Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

Keywords

HYDROLASE / SHIP2 / Phosphatase / C2 / phosphatidylinositol (3 / 4 / 5)-triphosphate

Function / homology

Function and homology information

negative regulation of insulin-like growth factor receptor signaling pathway / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / phosphatidylinositol dephosphorylation / regulation of actin filament organization / endochondral ossification / phosphatidylinositol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Le Coq, J. / Lietha, D.

Citation

Journal: Elife / Year: 2017
Title: Structural basis for interdomain communication in SHIP2 providing high phosphatase activity.
Authors: Le Coq, J. / Camacho-Artacho, M. / Velazquez, J.V. / Santiveri, C.M. / Gallego, L.H. / Campos-Olivas, R. / Dolker, N. / Lietha, D.

History

Deposition	Jul 25, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5okm.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb5okm.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	5okm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5okm_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	5okm_full_validation.pdf.gz	2.1 MB	Display
Data in XML	5okm_validation.xml.gz	130.5 KB	Display
Data in CIF	5okm_validation.cif.gz	186.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/5okm ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5okm	HTTPS FTP

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Related structure data

Related structure data	5oknC 5okoC 5okpC 3nr8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5okn-5 5okn-1 5oko-2 5okn-8 5okn-2 5okn-4 5okn-3 7k7t-2 6a6x-d 5rxj-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (2) #19 - Jul 2001 Actin similarity (2) #44 - Aug 2003 Calmodulin similarity (1) #148 - Apr 2012 Ras Protein similarity (2) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

C: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

D: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

E: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

F: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

G: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

H: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

425 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

defined by author&software
Evidence: gel filtration, protein elutes as a monomer
53.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

3

C: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

4

D: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

5

E: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

6

F: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

7

G: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

8

H: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	136.037, 175.836, 176.893
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing ...Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing inositol 5'-phosphatase 2 / SHIP-2 Mass: 52750.504 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: The two first residues are from the expression vector Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1564 / 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: 2.54 Å³/Da / Density % sol: 51.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1 M BisTris propane pH 7, 0.2 M NaNO3, 20% PEG 3350, 0.025% CH2Cl2, 2 mM TCEP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.96→48.97 Å / Num. obs: 287002 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.999 / R_pim(I) all: 0.033 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.96→1.99 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / CC_1/2: 0.743 / R_pim(I) all: 0.368 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NR8

3nr8

Resolution: 1.96→48.96 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.943 / SU B: 7.466 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2075	15180	5 %	RANDOM
R_work	0.1795	-	-	-
obs	0.18091	287002	99.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 45.654 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.12 Å²	0 Å²	0 Å²
2-	-	-0.15 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: 1 / Resolution: 1.96→48.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28047	0	225	1564	29836

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	29007
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	26443
X-RAY DIFFRACTION	r_angle_refined_deg	1.306	1.948	39239
X-RAY DIFFRACTION	r_angle_other_deg	1.241	3.002	61374
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.198	5	3473
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.215	23.835	1408
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.663	15	4995
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.696	15	191
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	4293
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	31858
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	6217
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.38	2.13	13875
X-RAY DIFFRACTION	r_mcbond_other	1.38	2.13	13874
X-RAY DIFFRACTION	r_mcangle_it	2.42	3.176	17302
X-RAY DIFFRACTION	r_mcangle_other	2.42	3.177	17303
X-RAY DIFFRACTION	r_scbond_it	1.346	2.346	15132
X-RAY DIFFRACTION	r_scbond_other	1.346	2.346	15132
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.362	3.434	21920
X-RAY DIFFRACTION	r_long_range_B_refined	5.622	24.578	31304
X-RAY DIFFRACTION	r_long_range_B_other	5.614	24.254	31066
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.96→2.011 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	1083	-
R_work	0.276	21111	-
obs	-	-	99.99 %

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	0.2534	-0.1137	0.1562	0.5673	-0.1415	0.7847	0.0047	0.0251	0.0344	0.0134	0.0585	-0.0385	0.0965	-0.0829	-0.0631	0.3488	0.0156	0.005	0.2545	0.0191	0.094	5.894	42.354	29.838
2	0.5226	0.1757	-0.0871	0.3129	-0.0829	0.8769	0.031	-0.0884	0.0366	-0.0468	-0.0496	-0.0581	-0.0489	-0.1043	0.0186	0.3316	0.0428	0.0476	0.2588	0.0173	0.1131	8.49	58.005	63.222
3	0.3972	-0.105	0.0956	0.6	0.1419	0.7872	0.1166	0.0916	0.0509	-0.0369	-0.1078	-0.0408	-0.0306	0.0256	-0.0088	0.3558	0.0677	0.0431	0.2805	0.0121	0.0738	66.017	45.952	29.647
4	0.8222	0.5375	0.4338	0.7457	0.1433	0.6119	0.251	-0.0657	0.0666	0.1038	-0.052	0.0624	0.1447	-0.0334	-0.199	0.3872	-0.0506	-0.0137	0.1534	-0.0222	0.1694	-26.88	68.771	16.146
5	0.5724	-0.115	-0.0558	0.7772	-0.1944	0.4686	-0.0433	0.0241	0.0479	0.117	-0.0379	-0.0053	0.0297	0.0184	0.0812	0.3863	0.0276	0.0275	0.1709	0.0132	0.1481	28.233	104.081	2.496
6	0.4398	-0.0852	0.0318	0.9936	-0.3006	0.3539	-0.0421	-0.0311	-0.0273	-0.2229	0.0556	-0.1112	0.0863	-0.0559	-0.0136	0.4199	0.0394	0.076	0.1526	0.0123	0.1521	27.185	71.112	-14.055
7	0.4931	-0.2022	0.0291	0.629	0.3195	0.8423	-0.0693	0.0265	-0.0137	0.1167	-0.0871	0.1197	-0.0138	0.097	0.1564	0.351	-0.0196	0.0002	0.159	-0.0227	0.1935	35.747	-12.83	0.887
8	0.5113	0.1356	0.0213	0.2794	0.0141	0.8737	0.0658	-0.0601	-0.0635	-0.0306	-0.101	-0.0156	0.0157	0.0648	0.0352	0.3342	0.0247	-0.0378	0.2639	0.0014	0.1067	62.281	27.058	61.36
9	1.9252	-0.275	-0.6898	1.5742	1.1324	0.9455	-0.0141	-0.0177	-0.1645	0.0396	-0.0543	0.0325	0.0409	-0.0152	0.0684	0.4284	0.0604	0.0588	0.1502	-0.0134	0.1358	22.51	17.349	15.858
10	2.2962	-1.6289	0.679	2.3185	-1.0302	1.1702	0.1063	0.3075	0.2474	-0.0486	-0.0134	-0.1056	-0.0694	0.1177	-0.0929	0.3275	0.0015	0.0871	0.2728	0.071	0.1568	39.551	61.67	50.691
11	6.4343	3.7429	-1.0184	6.2528	-2.5141	1.4092	-0.1093	-0.2329	0.7057	-0.3138	0.0666	0.6071	-0.2048	-0.0557	0.0427	0.5981	0.1716	-0.1459	0.1853	0.0692	0.3047	52.235	73.746	17.689
12	1.4921	-0.1606	-1.1145	1.0545	0.7184	1.5171	0.0926	-0.1736	0.1443	0.0446	-0.185	-0.0038	-0.0934	0.0999	0.0924	0.3811	-0.0351	-0.0317	0.2012	-0.0501	0.1793	3.241	82.709	19.312
13	3.3263	-1.8361	-1.3353	1.6418	2.0973	3.4891	-0.2518	-0.2632	-0.1789	0.1306	0.2115	0.0746	0.0438	0.1719	0.0403	0.7036	0.2377	0.1244	0.2412	0.0102	0.0374	11.042	116.276	27.992
14	1.9223	0.4566	-0.8145	0.7486	-0.7303	1.1903	-0.077	0.2938	0.312	-0.017	-0.0945	0.0393	0.0277	-0.1037	0.1715	0.377	0.0371	-0.0957	0.2463	0.0178	0.2785	-4.653	81.546	-17.305
15	4.0347	-1.6723	1.4487	1.5532	-2.5896	5.1253	0.1321	-0.4418	-0.0551	-0.1028	0.2186	0.1752	0.1443	-0.1948	-0.3507	0.5981	0.009	-0.1096	0.2905	0.0969	0.078	48.502	-27.851	27.421
16	1.3818	-0.8983	-0.2763	1.1317	0.2928	0.6092	0.1271	0.1854	-0.218	-0.097	-0.0118	0.2335	-0.018	0.0445	-0.1154	0.3249	0.0328	-0.0831	0.2555	-0.0526	0.1768	31.114	25.114	49.76

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	420 - 732
2	X-RAY DIFFRACTION	2	B	420 - 731
3	X-RAY DIFFRACTION	3	C	420 - 731
4	X-RAY DIFFRACTION	4	D	421 - 731
5	X-RAY DIFFRACTION	5	E	420 - 731
6	X-RAY DIFFRACTION	6	F	421 - 731
7	X-RAY DIFFRACTION	7	G	421 - 731
8	X-RAY DIFFRACTION	8	H	422 - 731
9	X-RAY DIFFRACTION	9	A	746 - 875
10	X-RAY DIFFRACTION	10	B	745 - 874
11	X-RAY DIFFRACTION	11	C	744 - 875
12	X-RAY DIFFRACTION	12	D	745 - 874
13	X-RAY DIFFRACTION	13	E	746 - 873
14	X-RAY DIFFRACTION	14	F	746 - 874
15	X-RAY DIFFRACTION	15	G	746 - 874
16	X-RAY DIFFRACTION	16	H	746 - 874

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