PDB-4nx8: Structure of a PTP-like phytase from Bdellovibrio bacteriovorus

ID or keywords:

Entry

Database: PDB / ID: 4nx8

Title

Structure of a PTP-like phytase from Bdellovibrio bacteriovorus

Components

Protein-tyrosine phosphatase 2

Keywords

HYDROLASE / PTP-like phytase /

phytase / inositol phosphatase /

protein tyrosine phosphatase

Function / homology

Function and homology information

protein-tyrosine-phosphatase /

protein tyrosine phosphatase activity
Similarity search - Function

Biological species

Bdellovibrio bacteriovorus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.698 Å

Authors

Gruninger, R.J. / Lovering, A.L.

Citation

Journal: Plos One / Year: 2014
Title: Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.
Authors: Gruninger, R.J. / Thibault, J. / Capeness, M.J. / Till, R. / Mosimann, S.C. / Sockett, R.E. / Selinger, B.L. / Lovering, A.L.

History

Deposition	Dec 8, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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	4nx8.cif.gz	240.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4nx8.ent.gz	194.8 KB	Display	PDB format
PDBx/mmJSON format	4nx8.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/nx/4nx8 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nx8	HTTPS FTP

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Related structure data

Related structure data	2pszS S: Starting model for refinement
Similar structure data	4esi-d 4gki-4 1zdt-2 2ai1-d 1il3-d 3a01-1 4gki-9 4few-3 4ple-1 1zh7-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#225 - Sep 2018 Phytase similarity (7) #126 - Jun 2010 Epidermal Growth Factor similarity (6) #145 - Jan 2012 Messenger RNA Capping similarity (5)

Deposited unit

A: Protein-tyrosine phosphatase 2

B: Protein-tyrosine phosphatase 2

hetero molecules

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

1

A: Protein-tyrosine phosphatase 2

hetero molecules

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

2

B: Protein-tyrosine phosphatase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.640, 78.560, 69.820
Angle α, β, γ (deg.)	90.000, 93.130, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein-tyrosine phosphatase 2 Mass: 33600.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd1204 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6MNP0, protein-tyrosine-phosphatase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.19 Å³/Da / Density % sol: 43.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 mM MgCl2, 100 mM Tris-HCl (7.0), 8-10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 10, 2010

Radiation

Monochromator: ACCEL/BRUKER double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.698→34.222 Å / Num. all: 63333 / Num. obs: 63333 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / B_iso Wilson estimate: 24 Å² / R_sym value: 0.078 / Net I/σ(I): 7.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.698-1.79	3.1	0.433	1.4	27255	8858	0.433	94.7
1.79-1.9	3.4	0.284	1.5	29533	8712	0.284	100
1.9-2.03	3.4	0.177	3.3	28117	8275	0.177	100
2.03-2.19	3.4	0.119	5.5	26326	7720	0.119	100
2.19-2.4	3.4	0.102	4.1	24141	7060	0.102	100
2.4-2.68	3.4	0.081	8	22130	6450	0.081	100
2.68-3.1	3.4	0.072	8.7	19430	5653	0.072	100
3.1-3.8	3.4	0.076	8	16614	4823	0.076	100
3.8-5.37	3.4	0.061	10	12828	3729	0.061	99.8
5.37-34.222	3.4	0.054	9.6	6882	2053	0.054	98.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.15	data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.11	data extraction
MxDC		data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2PSZ

2psz

Resolution: 1.698→34.222 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.21 / σ(F): 1.35 / σ(I): 1.5 / Phase error: 19.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1928	3211	5.07 %	Random
R_work	0.1563	-	-	-
all	0.1585	63333	-	-
obs	0.1581	63305	99.14 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 104.04 Å² / B_iso mean: 31.8236 Å² / B_iso min: 13.61 Å²

Refinement step

Cycle: LAST / Resolution: 1.698→34.222 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4241	0	9	561	4811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	4440
X-RAY DIFFRACTION	f_angle_d	1.648	6036
X-RAY DIFFRACTION	f_chiral_restr	0.086	643
X-RAY DIFFRACTION	f_plane_restr	0.009	787
X-RAY DIFFRACTION	f_dihedral_angle_d	13.962	1697

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.698-1.7234	0.3051	126	0.2766	2308	2434	88
1.7234-1.7503	0.3232	133	0.2664	2471	2604	94
1.7503-1.779	0.2593	154	0.2409	2617	2771	100
1.779-1.8097	0.3131	142	0.2122	2606	2748	100
1.8097-1.8426	0.271	142	0.197	2654	2796	100
1.8426-1.878	0.2191	159	0.1858	2562	2721	100
1.878-1.9163	0.2272	148	0.1665	2613	2761	100
1.9163-1.958	0.2194	128	0.1554	2642	2770	100
1.958-2.0035	0.1887	137	0.1561	2625	2762	100
2.0035-2.0536	0.1954	122	0.1654	2677	2799	100
2.0536-2.1092	0.2227	135	0.1655	2617	2752	100
2.1092-2.1712	0.185	134	0.1528	2615	2749	100
2.1712-2.2413	0.1856	135	0.1471	2659	2794	100
2.2413-2.3214	0.2161	145	0.1562	2633	2778	100
2.3214-2.4143	0.2043	158	0.1572	2587	2745	100
2.4143-2.5241	0.2178	119	0.1505	2666	2785	100
2.5241-2.6572	0.1924	147	0.1618	2618	2765	100
2.6572-2.8236	0.2162	131	0.1621	2665	2796	100
2.8236-3.0415	0.1787	127	0.1484	2648	2775	100
3.0415-3.3473	0.1746	167	0.1471	2621	2788	100
3.3473-3.8311	0.178	141	0.1404	2648	2789	100
3.8311-4.8246	0.1553	138	0.1319	2653	2791	100
4.8246-34.2288	0.1702	143	0.1588	2689	2832	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	0.2928	0.2232	-0.019	0.4951	0.0262	0.2139	-0.1601	0.236	0.2467	-0.2343	0.2029	0.2321	-0.1443	0.0458	-0.0641	0.2699	-0.0801	-0.0546	0.3309	0.0567	0.2083	18.0521	-19.4355	16.2027
2	0.1573	0.0514	-0.0174	0.1075	-0.0209	0.0638	-0.1382	0.1628	0.1847	-0.1623	0.1296	0.1662	-0.1631	0.0173	-0.0047	0.1797	-0.0369	-0.0112	0.1871	0.0287	0.2208	17.5591	-21.3185	24.4126
3	0.0354	-0.026	-0.0608	0.1513	-0.0116	0.1015	-0.0689	-0.0365	0.0057	-0.0127	-0.0197	0.1012	-0.0315	-0.0821	0	0.1538	-0.0057	0.0009	0.1861	0.0052	0.2162	13.0532	-30.384	30.8358
4	0.2152	0.1344	0.1462	0.3001	0.0791	0.2777	-0.1709	0.2708	0.0236	-0.2603	0.2467	0.0994	-0.0652	0.1336	0.032	0.2416	-0.0756	0.0127	0.2534	0.0146	0.1845	27.7601	-19.7523	16.7915
5	0.122	-0.0326	-0.0316	0.0826	0.0121	0.0126	0.0075	0.1892	0.129	-0.333	0.1202	-0.0297	-0.1191	0.0801	0.1238	0.833	-0.4467	-0.0208	0.4899	0.3537	0.1351	30.2108	-5.3424	6.3408
6	0.1706	0.0588	0.0227	0.0226	0.0171	0.0347	0.0656	0.1997	0.2518	-0.0374	0.1348	0.1169	-0.0943	-0.0471	-0.0041	0.7418	0.0473	-0.1094	0.295	0.1354	0.7437	19.3808	1.2198	20.5721
7	0.5617	0.1018	0.1875	0.1327	0.2493	0.7322	-0.1816	0.336	0.2594	-0.2952	0.2319	-0.0512	-0.3954	0.5212	-0.0488	0.3336	-0.1521	0.0394	0.2638	0.0209	0.2376	36.9697	-7.6049	20.1358
8	0.0589	-0.0228	0.0505	0.1701	-0.0619	0.0339	-0.0949	-0.1215	-0.332	0.0488	0.086	0.2571	0.189	0.0382	-0.0021	0.2225	0.0408	0.0278	0.2753	0.0411	0.2666	43.207	-18.9451	44.8524
9	0.0648	0.0694	0.0333	0.1834	-0.0302	0.0735	-0.0884	-0.4637	0.0073	0.2697	0.1303	0.0801	0.1546	0.0658	-0.0074	0.3654	0.1266	0.052	0.4357	0.0125	0.1786	46.1142	-12.5186	61.8371
10	0.078	0.0159	-0.0271	0.0379	-0.0003	0.018	-0.1796	-0.3723	0.0194	0.2456	0.1867	0.0338	-0.0828	-0.1207	0.0048	0.2798	0.1208	-0.0127	0.3218	-0.0369	0.1737	49.7571	-9.3254	56.2243
11	0.0728	0.0425	0.0033	0.0237	-0.0165	0.0242	-0.0151	-0.1428	-0.1528	0.0887	-0.0383	0.1156	0.1224	-0.1146	-0.0001	0.198	0.0139	0.0363	0.182	0.0089	0.2476	38.0017	-12.6247	43.9059
12	0.0341	-0.0206	0.0212	0.0181	0.0086	0.0244	0.0205	0.0807	0.0158	-0.0958	-0.021	-0.0497	-0.0056	0.0518	-0	0.1872	0.0062	0.0046	0.1843	0.0116	0.2156	48.0711	-10.8534	36.4361
13	0.0582	-0.1073	0.0229	0.167	0.1482	0.2758	-0.0461	-0.1462	0.0102	0.1207	0.0415	0.0828	0.0224	-0.0462	-0.0003	0.1462	0.0395	-0.0001	0.1687	-0.0097	0.1811	48.4872	-9.1659	47.0131
14	0.2907	-0.1772	0.165	0.5416	-0.0545	0.2002	-0.2302	-0.5181	-0.0706	0.3981	0.2071	0.1179	0.0836	0.0829	0.0378	0.3221	0.1084	-0.0116	0.335	0.0244	0.1515	54.1312	-17.5462	57.5012
15	0.1113	0.0743	0.05	0.0591	0.0448	0.0374	0.1097	-0.1716	-0.1214	0.179	0.0561	0.0284	0.1646	-0.0266	0.1527	0.6231	0.2939	0.0001	0.5601	0.3813	0.1192	57.0982	-28.9103	63.5065
16	0.0201	0.0028	0.0114	0.0038	0.0005	0.0072	0.0575	-0.3104	-0.321	0.0307	0.0453	0.1284	0.0506	-0.0323	0.0002	0.6793	-0.027	0.003	0.3256	0.1159	0.6393	46.2654	-35.6517	49.4356
17	0.2238	-0.0644	-0.204	0.0167	0.0623	0.1895	-0.1013	-0.286	-0.3554	0.1917	0.1341	0.0249	0.2971	0.2431	-0.1327	0.4055	0.1638	-0.0268	0.1763	0.0911	0.288	58.7878	-30.463	49.5794
18	0.0581	0.0417	-0.0345	0.0398	-0.0381	0.0359	-0.0868	-0.1617	0.1244	0.1625	-0.0438	-0.3151	-0.0609	0.2812	-0.005	0.3023	0.1101	-0.0721	0.4593	-0.054	0.2567	70.5772	-21.9681	49.899

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 91 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 92 through 127 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 128 through 158 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 225 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 226 through 242 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 243 through 257 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 258 through 293 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 33 through 62 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 63 through 84 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 85 through 104 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 105 through 120 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 121 through 141 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 142 through 194 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 195 through 225 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 226 through 242 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 243 through 257 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 258 through 278 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 279 through 293 )	B

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