PDB-5okn: Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant

ID or keywords:

Entry

Database: PDB / ID: 5okn

Title

Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant

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 / regulation of actin filament organization / phosphatidylinositol dephosphorylation / 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: 2.65 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	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5okn.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5okn.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5okn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5okn_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	5okn_full_validation.pdf.gz	2.1 MB	Display
Data in XML	5okn_validation.xml.gz	112.4 KB	Display
Data in CIF	5okn_validation.cif.gz	153.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/5okn ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5okn	HTTPS FTP

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Related structure data

Related structure data	5okmC 5okoC 5okpC C: citing same article (ref.)
Similar structure data	5okm-3 5okm-1 5okm-7 5okm-4 5oko-2 5okm-6 5rxj-d 5oko-1 5rxp-d 5rwe-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

5okmC

5okoC

5okpC

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, The protein elutes as a monomer
53.1 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
53.1 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
53.2 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
53.4 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
52.9 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
53.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	137.065, 177.143, 177.371
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 8 molecules ABCDEFGH

#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: 52706.492 Da / Num. of mol.: 8 / Mutation: D607A Source method: isolated from a genetically manipulated source Details: The first two residues are from the expression vector in which the gene was cloned. Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2(DE3)pLysS References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase

#1: Protein

Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing ...

Mass: 52706.492 Da / Num. of mol.: 8 / Mutation: D607A
Source method: isolated from a genetically manipulated source
Details: The first two residues are from the expression vector in which the gene was cloned.
Source: (gene. exp.)

Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2(DE3)pLysS
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase

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Non-polymers , 5 types, 320 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.59 Å³/Da / Density % sol: 52.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane, pH 7.0, 0.4 M KSCN, 20% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.65→49.17 Å / Num. obs: 119204 / % possible obs: 100 % / Redundancy: 9 % / CC_1/2: 0.996 / R_pim(I) all: 0.055 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.2 / CC_1/2: 0.7 / R_pim(I) all: 0.467 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→49.17 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.898 / SU B: 25.312 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.32 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24463	6370	5.1 %	RANDOM
R_work	0.206	-	-	-
obs	0.20796	119204	99.94 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 60.007 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.5 Å²	0 Å²	0 Å²
2-	-	-1.11 Å²	0 Å²
3-	-	-	-0.39 Å²

Refinement step

Cycle: 1 / Resolution: 2.65→49.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27549	0	237	284	28070

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	28386
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	25883
X-RAY DIFFRACTION	r_angle_refined_deg	1.267	1.949	38365
X-RAY DIFFRACTION	r_angle_other_deg	2.02	3.002	60025
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.279	5	3363
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.461	23.782	1367
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.247	15	4873
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.996	15	185
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	4218
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	31001
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	6080
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	1.321	3.153	13578
X-RAY DIFFRACTION	r_mcbond_other	1.321	3.153	13577
X-RAY DIFFRACTION	r_mcangle_it	2.422	4.708	16896
X-RAY DIFFRACTION	r_mcangle_other	2.422	4.708	16897
X-RAY DIFFRACTION	r_scbond_it	0.996	3.304	14808
X-RAY DIFFRACTION	r_scbond_other	0.996	3.304	14808
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.849	4.896	21469
X-RAY DIFFRACTION	r_long_range_B_refined	4.607	34.384	29240
X-RAY DIFFRACTION	r_long_range_B_other	4.607	34.385	29241
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.4	458	-
R_work	0.379	8712	-
obs	-	-	99.98 %

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	0.6062	0.1992	0.1106	1.0383	-0.2138	0.7328	-0.0048	-0.0709	-0.0018	-0.0639	0.0932	0.0124	-0.053	0.0383	-0.0884	0.2975	-0.0477	0.0079	0.4049	-0.0088	0.2115	-62.5199	46.2515	-29.7016
2	0.5886	-0.0797	-0.09	0.3551	-0.1676	1.2739	0.0712	0.0847	-0.0643	0.0209	-0.0987	-0.0245	0.0346	-0.1181	0.0275	0.3071	-0.0185	-0.0587	0.3887	-0.0229	0.241	-59.7685	29.8202	-62.7144
3	0.7685	0.6296	-0.2338	1.3815	0.4693	0.826	-0.0113	-0.1069	0.0281	-0.0444	0.0093	-0.1198	0.1791	0.0218	0.0019	0.374	-0.0245	-0.0344	0.372	0.0165	0.1779	-2.2814	42.2477	-29.3913
4	0.8749	-0.2864	-0.2036	0.8269	0.1872	0.3582	0.0767	0.0297	0.0879	-0.0422	0.0306	0.1275	0.0804	0.0467	-0.1073	0.2672	0.0029	-0.0009	0.2796	-0.0177	0.3887	-95.811	18.8844	-16.7765
5	0.6025	0.2523	0.3872	0.6368	-0.0701	1.1675	-0.1231	-0.0449	-0.0313	-0.1181	-0.0773	-0.0251	-0.0434	0.005	0.2004	0.3418	-0.0116	-0.0329	0.2803	0.0005	0.3017	-39.9725	-16.4156	-2.4584
6	0.6556	0.0699	0.0563	1.2553	-0.1182	0.2584	0.0122	-0.0313	0.0744	0.0889	0.0511	-0.135	0.0327	-0.0747	-0.0633	0.3304	-0.018	-0.0698	0.2772	0.0023	0.324	-41.8336	16.561	14.737
7	0.1738	0.1345	-0.1401	1.2966	0.7052	1.0574	-0.0037	-0.1819	0.04	-0.3795	-0.1745	0.1268	-0.026	0.1047	0.1782	0.4495	0.0576	-0.0566	0.211	-0.0319	0.3128	-32.5726	101.5718	-0.6412
8	0.7934	0.0557	-0.0878	0.2484	0.152	1.1688	0.146	0.0303	0.0331	-0.0046	-0.1392	-0.0066	-0.0404	0.1101	-0.0068	0.32	-0.0247	0.0647	0.4009	0.0018	0.2188	-5.5654	60.9105	-61.4175
9	4.0669	-0.3576	0.5586	1.9301	1.1419	0.8267	-0.1808	0.0374	0.1985	-0.0354	0.0902	0.0271	-0.056	0.0466	0.0906	0.2927	-0.083	-0.1019	0.2857	-0.0209	0.3266	-45.9333	71.327	-15.7816
10	1.9803	1.4413	-0.8129	2.0518	-1.2496	1.4915	0.0858	-0.2309	-0.2291	0.0179	-0.0654	-0.1057	-0.0177	0.1531	-0.0203	0.3098	0.0282	-0.0594	0.368	0.0582	0.252	-28.84	26.5984	-50.6844
11	3.9841	-1.5267	0.17	3.1891	-1.3147	0.6116	-0.0632	-0.1688	-0.6267	0.1425	0.0204	0.1566	-0.0608	0.0099	0.0428	0.4714	-0.1234	0.0719	0.1742	0.0711	0.2958	-17.0029	14.7966	-17.511
12	1.9173	0.9645	1.1303	1.1676	1.1716	2.0046	-0.0106	0.1964	-0.2755	0.0072	-0.015	-0.0499	0.04	0.2027	0.0257	0.2664	0.0788	0.0157	0.326	-0.0909	0.3473	-65.434	5.6111	-19.5664
13	3.9696	1.0526	0.5941	0.8206	1.3585	2.7614	-0.1173	0.1385	0.0929	-0.0567	0.057	0.0398	-0.0187	0.028	0.0603	0.4059	-0.1262	-0.0721	0.2765	-0.0171	0.1753	-57.2884	-28.4636	-28.1611
14	1.6402	-0.2849	1.2642	1.2434	-1.0134	1.5615	0.0664	-0.2292	-0.132	0.0213	-0.0839	-0.0418	0.0257	-0.2078	0.0175	0.3038	-0.0517	0.0535	0.3818	0.0172	0.314	-73.5498	6.4579	17.1098
15	1.9959	0.976	-0.6269	0.5917	-0.4272	0.5141	-0.2061	0.1249	0.0113	-0.1528	0.316	0.0568	-0.1289	-0.2175	-0.1099	0.6035	-0.1588	0.0775	0.4495	0.0777	0.0665	-20.4328	116.0691	-27.187
16	1.8944	0.9988	0.7341	2.1273	0.9835	1	-0.0324	-0.2138	0.176	0.2064	0.0845	0.3257	0.0447	0.0491	-0.0521	0.3111	-0.0036	0.141	0.3148	-0.0526	0.3186	-36.7747	63.4861	-49.7022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	421 - 733
2	X-RAY DIFFRACTION	2	B	420 - 732
3	X-RAY DIFFRACTION	3	C	422 - 731
4	X-RAY DIFFRACTION	4	D	420 - 731
5	X-RAY DIFFRACTION	5	E	420 - 731
6	X-RAY DIFFRACTION	6	F	420 - 731
7	X-RAY DIFFRACTION	7	G	421 - 730
8	X-RAY DIFFRACTION	8	H	421 - 731
9	X-RAY DIFFRACTION	9	A	746 - 875
10	X-RAY DIFFRACTION	10	B	746 - 874
11	X-RAY DIFFRACTION	11	C	747 - 875
12	X-RAY DIFFRACTION	12	D	745 - 874
13	X-RAY DIFFRACTION	13	E	745 - 874
14	X-RAY DIFFRACTION	14	F	746 - 874
15	X-RAY DIFFRACTION	15	G	748 - 872
16	X-RAY DIFFRACTION	16	H	746 - 874

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Protein , 1 types, 8 molecules ABCDEFGH

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