PDB-3pu9: Crystal structure of serine/threonine phosphatase Sphaerobacter t...

ID or keywords:

Entry

Database: PDB / ID: 3pu9

Title

Crystal structure of serine/threonine phosphatase Sphaerobacter thermophilus DSM 20745

Components

Protein serine/threonine phosphatase

Keywords

TRANSFERASE / PSI-biology / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / PP2C-like superfamily

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Sphaerobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Nocek, B. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of serine/threonine phosphatase Sphaerobacter thermophilus DSM 20745
Authors: Nocek, B. / Tesar, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Dec 3, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 8, 2012	Group: Other
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pu9.cif.gz	204.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3pu9.ent.gz	166.4 KB	Display	PDB format
PDBx/mmJSON format	3pu9.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/pu/3pu9 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3pu9	HTTPS FTP

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Related structure data

Similar structure data	3usk-3 5n9w-2 3usk-2 3usk-1 4ler-d 3gww-d 3mx3-1 3uso-1 3uso-2 7dii-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
Other databases	TargetTrack: apc100730

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein serine/threonine phosphatase

B: Protein serine/threonine phosphatase

hetero molecules

51.4 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)	60.168, 54.713, 63.262
Angle α, β, γ (deg.)	90.00, 99.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein serine/threonine phosphatase Mass: 25608.252 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_0969 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: D1C2D8
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.66 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 30% pag 400, 0.1 Ches, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.55→40 Å / Num. all: 59002 / Num. obs: 58016 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 26
Reflection shell	Resolution: 1.55→1.58 Å / % possible all: 97.3

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
ARP/wARP		model building
CCP4		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→40 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.861 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21688	2932	5.1 %	RANDOM
R_work	0.17771	-	-	-
all	0.183	57893	-	-
obs	0.17987	54961	98.13 %	-

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 mean: 23.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	-1 Å²
2-	-	0.89 Å²	0 Å²
3-	-	-	-1.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3446	0	10	333	3789

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	3590
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2476
X-RAY DIFFRACTION	r_angle_refined_deg	1.769	1.991	4860
X-RAY DIFFRACTION	r_angle_other_deg	1.595	3	5997
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.456	5	492
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.018	21.806	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.729	15	591
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.066	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	571
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4116
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	744
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	2.093	1.5	2372
X-RAY DIFFRACTION	r_mcbond_other	4.847	1.5	996
X-RAY DIFFRACTION	r_mcangle_it	3.306	2	3780
X-RAY DIFFRACTION	r_scbond_it	4.656	3	1218
X-RAY DIFFRACTION	r_scangle_it	7.162	4.5	1074
X-RAY DIFFRACTION	r_rigid_bond_restr	2.382	3	3572
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	202	-
R_work	0.261	3996	-
obs	-	-	96.35 %

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	0.835	0.2472	0.8921	0.1213	0.4372	2.0713	0.0096	0.0424	-0.043	0.0226	0.0013	0.0008	-0.0096	0.0032	-0.0109	0.1903	0.0023	0.0086	0.212	-0.0003	0.2151	15.2425	14.7888	45.8363
2	0.1709	0.0481	0.4244	0.2548	-0.0784	1.089	-0.0045	-0.0216	0.0249	0.0581	-0.0098	0.0444	-0.0527	-0.0367	0.0143	0.2171	0.0016	0.0119	0.2181	-0.001	0.2169	17.2293	22.7537	58.1144
3	0.2559	-0.1064	0.2087	0.1723	-0.016	0.4696	-0.0139	0.0014	0.0017	0.0141	-0.0098	0.0027	-0.0348	-0.0181	0.0237	0.2076	0.0017	0.0029	0.2071	-0.0002	0.2176	15.759	27.8823	49.0143
4	0.943	0.2756	-0.4192	0.1495	-0.2893	2.8669	0.0657	0.0196	0.0916	0.0186	0.0717	-0.0078	-0.1281	-0.0849	-0.1373	0.2113	0.0111	0.0081	0.2058	0.0102	0.2254	11.5335	34.7875	40.7721
5	0.3238	-0.0746	0.2116	0.1441	0.0577	0.6788	0.0093	-0.0183	0.0381	0.009	0.0036	-0.0035	-0.032	-0.0096	-0.0128	0.2165	-0.0017	0.0092	0.2058	-0.0048	0.2183	21.5906	39.2059	47.1411
6	0.2906	-0.2256	-0.0385	0.1305	-0.0315	0.1356	0.0381	0.0293	-0.0107	-0.0285	-0.0142	-0.0137	-0.0352	0.0121	-0.0238	0.2191	-0.0014	0.0055	0.2054	-0.0005	0.2104	19.9614	27.0845	39.6898
7	0.2914	0.1173	0.3712	0.7633	0.5424	1.2926	0.0006	0.0329	0.01	-0.0577	-0.0112	-0.0223	-0.0395	0.0329	0.0106	0.1963	0.0024	0.0117	0.2119	-0.002	0.2195	27.0459	14.2104	35.8482
8	0.2087	-0.3776	-0.2025	3.7631	1.132	0.3723	0.0078	0.0418	0.0076	-0.0609	0.0343	-0.1634	-0.0281	0.0197	-0.0421	0.1997	-0.0054	0.0102	0.2208	-0.0071	0.2233	29.9078	24.5966	41.3957
9	0.9788	1.0163	0.7394	1.5546	1.1435	1.046	-0.0304	0.0571	0.0389	-0.0966	0.0362	-0.0114	-0.0812	0.0518	-0.0058	0.2151	-0.0054	0.0112	0.203	0.0037	0.2137	26.5005	32.1196	37.6406
10	0.3468	-0.0587	0.4803	0.2169	0.0271	1.0646	0.0224	0.0375	-0.0572	0.0031	0.0331	-0.0601	0.0071	0.0888	-0.0556	0.1875	0.0002	0.0065	0.2165	-0.0059	0.2301	27.9103	12.7091	47.218
11	1.611	-1.2202	-0.5984	0.8253	0.2661	0.6082	0.0089	0.108	-0.1679	-0.0165	-0.0592	0.0809	0.0907	0.0585	0.0503	0.2073	0.0094	-0.0005	0.2072	-0.0159	0.231	23.9465	5.0961	41.8361
12	0.5502	-0.1205	0.54	0.3122	-0.2353	0.8625	0.0121	-0.0254	-0.0475	0.0169	-0.0066	-0.0047	0.0494	-0.0182	-0.0055	0.2059	0.002	0.0035	0.2079	0.0077	0.222	22.5052	8.0696	53.3162
13	0.6504	0.2207	1.2828	0.4083	0.6776	4.0106	-0.0041	-0.0011	-0.026	0.0046	-0.0298	-0.0128	0.0235	-0.0221	0.0339	0.1848	0.0006	0.0136	0.2067	-0.0002	0.2132	19.3202	14.6331	46.0152
14	0.9657	-1.2114	-2.1884	1.5094	2.2894	4.3265	-0.3953	-0.1366	-0.3342	-0.0866	0.319	0.0376	0.0429	0.1529	0.0763	0.2005	-0.1062	0.0939	0.4251	-0.1821	0.3876	1.8046	10.9583	32.0753
15	1.8693	-0.3466	2.4969	0.1225	-1.2698	7.8751	0.0276	-0.0206	-0.0563	0.0118	-0.0101	-0.0229	-0.0684	-0.1368	-0.0175	0.1862	0.0025	0.0086	0.2382	0.0089	0.2127	5.4925	15.2277	52.2442
16	0.2722	-0.0933	0.3528	0.0355	-0.4742	2.7257	0.0191	0.0518	-0.0466	-0.0079	0.0015	0.0067	-0.0582	0.1367	-0.0206	0.1958	-0.0017	0.0106	0.2264	-0.0055	0.2125	-1.8637	17.3464	42.873
17	0.1979	0.1344	0.1613	0.4278	0.0557	0.1946	-0.0103	0.0405	-0.0166	0.0397	0.023	-0.0261	-0.0092	0.0236	-0.0127	0.205	0.0022	-0.0042	0.2112	-0.0035	0.2184	1.0765	25.9256	49.0745
18	0.043	-0.5227	-0.9015	1.5741	1.2282	2.1955	0.0741	0.0285	-0.0125	-0.1581	-0.085	-0.0915	-0.1842	-0.1359	0.0109	0.2139	0.0134	0.007	0.2174	0.0047	0.2141	-3.1754	32.122	37.2568
19	1.4477	-0.6277	-0.2663	0.0285	0.8674	2.2346	-0.0117	-0.0376	0.1548	-0.0335	0.0727	-0.0528	-0.1293	0.0795	-0.061	0.2295	0.0008	-0.0008	0.1987	-0.0103	0.228	2.5697	34.8602	55.3681
20	0.4943	-0.5554	0.5428	1.3672	-0.867	0.8806	-0.0042	0.0263	0.027	0.0678	-0.0185	-0.0218	-0.0433	0.0158	0.0227	0.2088	0.0111	0.004	0.2109	0.0021	0.207	-6.1769	35.5352	47.9514
21	0.7803	-1.4297	-0.7201	0.7264	0.8196	0.314	-0.1745	-0.044	-0.0463	0.2432	0.1306	0.1852	0.0337	0.07	0.044	0.3072	0.0317	0.0147	0.2168	0.0239	0.2128	-5.7753	25.5231	58.6721
22	0.3803	-1.0251	1.3189	8.4779	-3.1449	4.036	-0.0558	-0.0106	-0.0526	-0.0585	-0.002	0.1824	-0.2294	-0.2321	0.0578	0.1985	0.0146	0.017	0.2335	0.0194	0.218	-14.9921	22.964	49.5401
23	1.3973	1.5595	3.5583	4.5518	-1.2105	7.2376	-0.4333	0.2973	0.2232	0.1077	0.1481	0.117	-0.6551	-0.2111	0.2852	0.2231	0.0012	-0.0152	0.2858	0.0682	0.2428	-14.8901	17.2588	57.6526
24	1.2008	-2.2234	-0.2493	4.3185	-0.5529	3.195	-0.0674	-0.0469	-0.0111	0.1865	0.1913	0.0528	-0.1702	-0.1279	-0.1239	0.2149	0.0301	0.0106	0.2165	0.0055	0.2028	-13.781	39.4384	49.2419
25	0.1165	0.0142	0.3168	0.283	-0.0202	0.8942	-0.0239	-0.0558	-0.0734	0.0415	0.0726	0.064	-0.1107	-0.152	-0.0487	0.2021	0.0125	0.0144	0.2302	0.0127	0.2168	-10.8638	19.0707	52.4879
26	1.0346	-0.416	1.6148	-0.0545	-1.375	2.8214	0.0564	0.0424	-0.066	0.0044	-0.117	-0.0232	0.1291	0.0349	0.0605	0.1839	-0.013	0.0176	0.3056	-0.03	0.2271	-20.8983	11.7377	40.5204
27	2.4718	0.5463	0.5087	0.4554	-0.4631	1.7354	0.1643	-0.0773	-0.1809	0.0169	-0.066	-0.0408	0.2778	-0.17	-0.0983	0.2433	-0.0389	-0.0212	0.1921	0.0187	0.2193	-9.9426	6.287	51.4865
28	1.0995	0.2564	1.0354	0.167	0.444	1.9697	-0.0017	0.0309	-0.0536	0.0491	0.0144	0.0172	0.1286	-0.0144	-0.0127	0.2085	-0.0082	0.0024	0.2063	-0.0013	0.2257	-8.1812	9.2699	42.0255
29	0.4142	-0.0623	0.4244	-0.0106	-0.0119	1.9565	-0.0002	0.0077	-0.0456	-0.006	0.0029	0.011	0.0895	0.0023	-0.0027	0.197	-0.0002	0.0087	0.2092	0.0013	0.223	-6.4784	14.1678	45.4868
30	0.5548	-0.0651	1.1837	0.1119	0.0761	3.3464	0.0198	-0.0206	-0.0604	0.0238	-0.0075	0.052	0.0565	-0.0561	-0.0123	0.1886	-0.0004	0.0101	0.2335	0.0024	0.2159	10.0171	12.8496	49.3947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 18
2	X-RAY DIFFRACTION	2	A	19 - 28
3	X-RAY DIFFRACTION	3	A	29 - 59
4	X-RAY DIFFRACTION	4	A	60 - 71
5	X-RAY DIFFRACTION	5	A	72 - 89
6	X-RAY DIFFRACTION	6	A	90 - 113
7	X-RAY DIFFRACTION	7	A	114 - 125
8	X-RAY DIFFRACTION	8	A	126 - 136
9	X-RAY DIFFRACTION	9	A	137 - 150
10	X-RAY DIFFRACTION	10	A	151 - 175
11	X-RAY DIFFRACTION	11	A	176 - 189
12	X-RAY DIFFRACTION	12	A	190 - 208
13	X-RAY DIFFRACTION	13	A	209 - 221
14	X-RAY DIFFRACTION	14	A	222 - 230
15	X-RAY DIFFRACTION	15	A	231 - 239
16	X-RAY DIFFRACTION	16	B	4 - 22
17	X-RAY DIFFRACTION	17	B	23 - 44
18	X-RAY DIFFRACTION	18	B	45 - 61
19	X-RAY DIFFRACTION	19	B	62 - 74
20	X-RAY DIFFRACTION	20	B	75 - 104
21	X-RAY DIFFRACTION	21	B	105 - 112
22	X-RAY DIFFRACTION	22	B	113 - 118
23	X-RAY DIFFRACTION	23	B	119 - 133
24	X-RAY DIFFRACTION	24	B	134 - 143
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