PDB-4xuu: The hSac2 domain from human phosphoinositide phosphatase Sac2

ID or keywords:

Entry

Database: PDB / ID: 4xuu

Title

The hSac2 domain from human phosphoinositide phosphatase Sac2

Components

Phosphatidylinositide phosphatase SAC2

Keywords

PROTEIN BINDING / Pleckstrin-homology domain / dimerization.

Function / homology

Function and homology information

phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol catabolic process / phosphatidylinositol phosphate 4-phosphatase activity / regulation of endocytic recycling / Synthesis of PIPs at the early endosome membrane / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.62 Å

Authors

Hsu, F. / Mao, Y.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structure of the hSac2 domain at 2.62
Authors: Hsu, F. / Mao, Y.

History

Deposition	Jan 26, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 2.0	Sep 13, 2017	Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Source and taxonomy Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 2.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4xuu_validation.pdf.gz	453.8 KB	Display	wwPDB validaton report
Full document	4xuu_full_validation.pdf.gz	468.5 KB	Display
Data in XML	4xuu_validation.xml.gz	25.9 KB	Display
Data in CIF	4xuu_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xu/4xuu ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xuu	HTTPS FTP

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Related structure data

Similar structure data	1ygu-2 4gj6-d 5xms-2 4pfn-1 4gj8-d 3b1c-1 4o6z-1 6ewj-1 4oyt-2 5yfy-2 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

Deposited unit

A: Phosphatidylinositide phosphatase SAC2

B: Phosphatidylinositide phosphatase SAC2

C: Phosphatidylinositide phosphatase SAC2

D: Phosphatidylinositide phosphatase SAC2

78.9 kDa, 4 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)	61.772, 82.852, 157.695
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 1 - 169 / Label seq-ID: 1 - 169

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D

#1: Protein	Phosphatidylinositide phosphatase SAC2 / Inositol polyphosphate 5-phosphatase F / Sac domain-containing inositol phosphatase 2 / Sac domain- ...Inositol polyphosphate 5-phosphatase F / Sac domain-containing inositol phosphatase 2 / Sac domain-containing phosphoinositide 5-phosphatase 2 / hSAC2 Mass: 19736.730 Da / Num. of mol.: 4 / Fragment: UNP residues 169-593 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5F, KIAA0966, SAC2, MSTP007, MSTP047 / Plasmid: pET28a Details (production host): Contains an N-terminal HIS-SUMO tag Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q9Y2H2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Phosphatidylinositide phosphatase SAC2 / Inositol polyphosphate 5-phosphatase F / Sac domain-containing inositol phosphatase 2 / Sac domain- ...

Mass: 19736.730 Da / Num. of mol.: 4 / Fragment: UNP residues 169-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: INPP5F, KIAA0966, SAC2, MSTP007, MSTP047 / Plasmid: pET28a
Details (production host): Contains an N-terminal HIS-SUMO tag
Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9Y2H2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.56 Å³/Da / Density % sol: 51.87 %
Crystal grow	Temperature: 300.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.0, and 20% PEG3350. Long rod-shaped crystals formed within 2-3 days. Temp details: Room temperature

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: A1 / Wavelength: 0.978 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Redundancy: 7.7 % / Number: 359545 / R_merge(I) obs: 0.067 / Χ²: 1.28 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 46680 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
7.05	50	1	0.047	1.139	7.3
5.6	7.05	1	0.054	1.286	7.7
4.89	5.6	1	0.048	1.332	7.7
4.45	4.89	1	0.051	1.564	7.6
4.13	4.45	1	0.049	1.544	7.7
3.88	4.13	1	0.051	1.599	7.7
3.69	3.88	1	0.057	1.62	7.7
3.53	3.69	1	0.071	1.575	7.7
3.39	3.53	1	0.073	1.637	7.7
3.28	3.39	1	0.082	1.613	7.7
3.17	3.28	1	0.103	1.504	7.7
3.08	3.17	1	0.129	1.284	7.8
3	3.08	1	0.158	1.216	7.8
2.93	3	1	0.199	1.101	7.8
2.86	2.93	1	0.224	1.017	7.8
2.8	2.86	1	0.322	0.945	7.8
2.74	2.8	1	0.387	0.92	7.8
2.69	2.74	1	0.431	0.884	7.8
2.64	2.69	1	0.569	0.917	7.7
2.6	2.64	1	0.613	0.905	7.6

Reflection

Resolution: 2.6→30 Å / Num. obs: 25539 / % possible obs: 99 % / Redundancy: 7.7 % / R_sym value: 0.067 / Net I/σ(I): 29

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.6-2.64	7.6	0.613	2396	0.905	100
2.64-2.69	7.7	0.569	2276	0.917	100
2.69-2.74	7.8	0.431	2360	0.884	100
2.74-2.8	7.8	0.387	2335	0.92	100
2.8-2.86	7.8	0.322	2337	0.945	100
2.86-2.93	7.8	0.224	2333	1.017	100
2.93-3	7.8	0.199	2337	1.101	100
3-3.08	7.8	0.158	2298	1.216	100
3.08-3.17	7.8	0.129	2390	1.284	100
3.17-3.28	7.7	0.103	2287	1.504	100
3.28-3.39	7.7	0.082	2373	1.613	100
3.39-3.53	7.7	0.073	2312	1.637	100
3.53-3.69	7.7	0.071	2318	1.575	100
3.69-3.88	7.7	0.057	2328	1.62	100
3.88-4.13	7.7	0.051	2356	1.599	100
4.13-4.45	7.7	0.049	2346	1.544	100
4.45-4.89	7.6	0.051	2325	1.564	100
4.89-5.6	7.7	0.048	2336	1.332	100
5.6-7.05	7.7	0.054	2327	1.286	100
7.05-50	7.3	0.047	2310	1.139	98

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.5.0110	refinement
PDB_EXTRACT	3.14	data extraction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.62→30 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.892 / SU B: 28.451 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.191 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2867	1261	5.1 %	RANDOM
R_work	0.2483	23529	-	-
obs	0.2502	24790	98.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 58.82 Å² / B_iso mean: 32.509 Å² / B_iso min: 10.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.36 Å²	0 Å²	0 Å²
2-	-	4.37 Å²	0 Å²
3-	-	-	-4.73 Å²

Refinement step

Cycle: final / Resolution: 2.62→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5434	0	0	22	5456
B_iso mean	-	-	-	34.8	-
Num. residues	-	-	-	-	671

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	5551
X-RAY DIFFRACTION	r_angle_refined_deg	0.894	1.988	7496
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.051	5	666
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.76	24.85	266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.727	15	1043
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.207	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	817
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	4163
X-RAY DIFFRACTION	r_mcbond_it	0.444	1.5	3358
X-RAY DIFFRACTION	r_mcangle_it	0.823	2	5422
X-RAY DIFFRACTION	r_scbond_it	0.818	3	2193
X-RAY DIFFRACTION	r_scangle_it	1.284	4.5	2074

Refine LS restraints NCS

Ens-ID: 1 / Number: 1302 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	MEDIUM POSITIONAL	0.61	0.5
2	B	MEDIUM POSITIONAL	0.62	0.5
3	C	MEDIUM POSITIONAL	0.6	0.5
4	D	MEDIUM POSITIONAL	0.8	0.5
1	A	MEDIUM THERMAL	0.19	2
2	B	MEDIUM THERMAL	0.13	2
3	C	MEDIUM THERMAL	0.14	2
4	D	MEDIUM THERMAL	0.15	2

LS refinement shell

Resolution: 2.619→2.686 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	81	-
R_work	0.324	1532	-
all	-	1613	-
obs	-	-	88.92 %

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	23.0299	5.9251	15.269	3.9582	3.6919	21.1193	-0.1066	-0.9428	-0.4643	0.4462	-0.1452	-0.4797	1.1497	1.7366	0.2518	0.412	0.1708	0.0265	0.699	0.1707	0.2966	51.3114	35.8029	22.5715
2	6.6841	-0.2152	-0.2016	9.7932	-2.7501	9.7484	0.1729	-0.3609	0.6835	0.1293	-0.0725	0.1398	-0.8832	-0.4272	-0.1003	0.1142	0.019	0.0692	0.0568	-0.0688	0.1631	39.7506	48.7652	6.2521
3	6.6342	1.9745	-0.4427	7.427	0.8049	8.7993	0.2159	-0.5908	0.8763	0.1839	0.0129	0.1719	-1.1369	-0.3071	-0.2287	0.2037	0.0072	0.0989	0.1001	-0.0798	0.2294	40.1207	50.9591	9.3623
4	5.1328	-0.9741	-1.0326	2.9618	-0.636	9.6611	0.2631	-0.028	0.5714	-0.0063	-0.0912	0.259	-0.8591	-0.8865	-0.1719	0.1549	0.0691	0.0809	0.0964	-0.0255	0.2316	34.8854	48.9089	2.426
5	5.2348	-0.257	-1.1208	4.2326	0.0446	8.4329	0.1932	0.3141	0.4613	-0.2975	-0.1509	0.0479	-0.6596	-0.735	-0.0423	0.1146	0.0785	0.0285	0.0824	0.0241	0.1912	37.1148	47.7903	-2.5394
6	19.5411	4.5416	-7.1208	2.9209	-3.9792	6.233	0.5581	-1.6531	0.8252	0.6082	0.1127	0.5862	-1.1198	0.1501	-0.6708	0.6113	0.0866	0.2719	0.5187	-0.0306	0.4008	42.3262	46.6635	22.0324
7	8.0215	-1.3625	-0.9106	10.2164	2.9347	9.0566	0.1298	-0.7349	-0.9077	0.4398	-0.0651	-0.1507	0.8456	1.1738	-0.0647	0.1455	0.0866	-0.0103	0.2987	0.1637	0.2294	57.0584	33.7028	8.176
8	6.4745	-0.1191	-1.0709	8.973	-1.3394	7.9621	-0.1587	-1.0181	-0.8937	0.3972	0.1285	0.0792	1.1973	0.9319	0.0303	0.2313	0.1389	0.0148	0.3634	0.1968	0.3071	56.0695	31.8787	11.2801
9	5.7626	-3.139	-2.6176	5.8275	0.3157	8.1238	0.097	-0.6857	-0.4287	-0.0894	-0.1602	-0.3999	0.4543	1.4421	0.0632	0.0535	0.1113	0.0105	0.5048	0.1124	0.2958	62.8178	33.8296	5.9363
10	5.7684	-2.1365	-0.4098	5.1834	-0.5808	6.7446	0.34	-0.0527	-0.2769	-0.4655	-0.2925	-0.2522	0.5293	1.3635	-0.0475	0.0998	0.1185	0.0591	0.361	0.0596	0.2963	61.8402	35.0204	0.677
11	20.8972	-4.7916	-9.4609	3.6499	1.4455	9.8567	0.2225	0.6865	0.4206	-0.2151	0.0407	-0.2403	-0.8191	-0.4121	-0.2631	0.4361	-0.0528	-0.115	0.4947	0.0363	0.1884	51.6225	47.7322	-50.0757
12	8.5447	0.1528	-2.3056	8.8636	-2.3827	9.5765	-0.2611	0.8265	-0.5044	0.2544	-0.0527	0.1274	0.6112	-0.8789	0.3138	0.3272	0.0194	-0.0607	0.2169	-0.1425	0.107	40.938	39.1502	-32.6495
13	6.1426	0.2606	-2.8817	6.8847	-0.3573	8.6558	-0.5439	1.0813	-0.7405	-0.7888	0.3304	-0.0427	1.2339	-1.1951	0.2135	0.4755	-0.1113	-0.0664	0.3957	-0.1911	0.2241	40.2416	35.3383	-36.1049
14	5.1256	0.5735	-1.0009	2.4209	-0.3549	8.7518	-0.2113	0.4261	-0.4874	-0.0763	0.1246	0.3191	1.0715	-1.2203	0.0867	0.4396	-0.0501	-0.0931	0.3025	-0.1002	0.241	35.203	36.2773	-28.9568
15	5.7648	1.4788	-2.1758	4.1409	-0.4341	9.4223	-0.2334	0.1689	-0.3242	0.188	0.0295	0.0926	0.876	-0.9393	0.2039	0.3423	0.0072	-0.0661	0.2037	-0.0631	0.1804	37.2684	37.9093	-24.2486
16	16.2292	0.2572	8.4131	3.8949	-1.3286	7.8964	-0.7047	0.5185	-0.5628	-0.2579	0.6929	0.7448	0.8051	-1.4953	0.0119	0.8417	-0.6172	-0.0049	1.2609	-0.1601	0.3703	42.6614	36.8316	-48.0835
17	6.5357	2.0731	-1.098	7.4519	1.0702	6.0609	0.0142	0.2988	0.5787	-0.1792	0.2165	0.2344	-0.228	0.4724	-0.2307	0.2738	0.0753	-0.0655	0.1668	0.0338	0.1216	57.4481	50.0568	-36.2069
18	6.1432	0.8869	0.0417	11.5828	-0.5191	8.2199	-0.0991	0.7224	0.7839	-0.5272	0.3346	0.2428	-1.0413	0.3785	-0.2355	0.354	0.0285	-0.0384	0.2208	0.0554	0.2273	56.5698	52.8184	-38.9352
19	3.8076	3.0029	0.9872	5.3718	2.7432	7.4072	-0.0088	0.2763	0.3014	0.264	0.22	-0.4286	-0.4983	1.1593	-0.2112	0.3582	0.0144	-0.1131	0.3272	-0.0266	0.2814	63.1741	51.387	-32.9701
20	4.9559	2.4287	0.8682	6.6952	0.9931	7.8428	0.2135	-0.322	0.2903	0.7334	0.0402	-0.2642	-0.2674	0.9767	-0.2537	0.2829	0.0269	-0.1092	0.2265	-0.0829	0.2504	62.278	50.539	-27.8677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 22
2	X-RAY DIFFRACTION	2	A	23 - 42
3	X-RAY DIFFRACTION	3	A	43 - 67
4	X-RAY DIFFRACTION	4	A	68 - 93
5	X-RAY DIFFRACTION	5	A	94 - 169
6	X-RAY DIFFRACTION	6	B	1 - 22
7	X-RAY DIFFRACTION	7	B	23 - 42
8	X-RAY DIFFRACTION	8	B	43 - 67
9	X-RAY DIFFRACTION	9	B	68 - 93
10	X-RAY DIFFRACTION	10	B	94 - 169
11	X-RAY DIFFRACTION	11	C	1 - 22
12	X-RAY DIFFRACTION	12	C	23 - 42
13	X-RAY DIFFRACTION	13	C	43 - 67
14	X-RAY DIFFRACTION	14	C	68 - 93
15	X-RAY DIFFRACTION	15	C	94 - 169
16	X-RAY DIFFRACTION	16	D	1 - 22
17	X-RAY DIFFRACTION	17	D	23 - 42
18	X-RAY DIFFRACTION	18	D	43 - 67
19	X-RAY DIFFRACTION	19	D	68 - 93
20	X-RAY DIFFRACTION	20	D	94 - 169

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