PDB-5k24: Crystal structure of the complex between phosphatase PRL-2 in the...

ID or keywords:

Entry

Database: PDB / ID: 5k24

Title

Crystal structure of the complex between phosphatase PRL-2 in the oxidized state with the Bateman domain of murine magnesium transporter CNNM3

Components

Metal transporter CNNM3
Protein tyrosine phosphatase type IVA 2

Keywords

HYDROLASE/TRANSPORTER PROTEIN/PROTEIN BINDING /

Complex /

phosphatase /

magnesium transporter /

protein binding /

HYDROLASE / HYDROLASE-TRANSPORTER PROTEIN-PROTEIN BINDING complex

Function / homology

Function and homology information

RAB geranylgeranylation / transmembrane transporter activity / monoatomic ion transport /

protein-tyrosine-phosphatase /

protein tyrosine phosphatase activity / membrane => GO:0016020 /

early endosome / intracellular membrane-bounded organelle /

nucleus /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.1 Å

Authors

Kozlov, G. / Gulerez, I. / Gehring, K.

Citation

Journal: Sci Rep / Year: 2017
Title: PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3.
Authors: Zhang, H. / Kozlov, G. / Li, X. / Wu, H. / Gulerez, I. / Gehring, K.

History

Deposition	May 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2018	Group: Data collection / Database references / Derived calculations Category: citation / citation_author / pdbx_struct_oper_list Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5k24.cif.gz	244.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k2/5k24 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k24	HTTPS FTP

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Related structure data

Related structure data	5k23C 5k25C 5tsrC 5k22 C: citing same article (ref.)
Similar structure data	4qpl-d 5tsr-d 6wur-1 6fxx-d 7aud-4 1f0k-d 1oak-d 5k25-1 2r3v-5 2r4s-d 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	#145 - Jan 2012 Messenger RNA Capping similarity (4) #126 - Jun 2010 Epidermal Growth Factor similarity (8) #140 - Aug 2011 Rhomboid Protease GlpG similarity (3) #225 - Sep 2018 Phytase similarity (3) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#145 - Jan 2012
Messenger RNA Capping
similarity (4)
#126 - Jun 2010
Epidermal Growth Factor
similarity (8)
#140 - Aug 2011
Rhomboid Protease GlpG
similarity (3)
#225 - Sep 2018
Phytase
similarity (3)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Protein tyrosine phosphatase type IVA 2

B: Protein tyrosine phosphatase type IVA 2

C: Metal transporter CNNM3

D: Metal transporter CNNM3

hetero molecules

76.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	154.222, 52.119, 102.855
Angle α, β, γ (deg.)	90.00, 106.02, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-501- FLC
2	1	D-501- FLC

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	5 - 152
2	1	B	5 - 152
1	2	C	318 - 451
2	2	D	318 - 451

NCS ensembles :

ID
1
2

#1: Protein	Protein tyrosine phosphatase type IVA 2 / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of regenerating liver 2 / PRL-2 Mass: 20893.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptp4a2, Prl2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O70274, protein-tyrosine-phosphatase
#2: Protein	Metal transporter CNNM3 / / Ancient conserved domain-containing protein 3 / mACDP3 / Cyclin-M3 Mass: 17341.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm3, Acdp3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q32NY4
#3: Chemical	ChemComp-FLC / CITRATE ANION / Citric acid Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M ammonium citrate, 19% PEG 3350, 10 mM L-cysteine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9773 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2014
Radiation	Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9773 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 13689 / % possible obs: 98.88 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / R_merge(I) obs: 0.078 / Net I/σ(I): 33.9
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.644 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0069	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 3.1→50 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.881 / SU B: 64.728 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.552

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30327	740	5.1 %	RANDOM
R_work	0.25242	-	-	-
obs	0.25534	13689	98.88 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 121.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9 Å²	0 Å²	0.8 Å²
2-	-	0.98 Å²	0 Å²
3-	-	-	-2.01 Å²

Refinement step

Cycle: 1 / Resolution: 3.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4509	0	13	0	4522

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.019	4620
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.837	1.978	6289
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	726
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3493
X-RAY DIFFRACTION	r_gen_planes_other
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	1.507	6.36	2288
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.639	9.541	2853
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.389	6.449	2332
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	6.572	63.399	5891
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	186	0.1
1	2	B	186	0.1
2	1	C	191	0.06
2	2	D	191	0.06

LS refinement shell

Resolution: 3.1→3.181 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.379	37	-
R_work	0.339	913	-
obs	-	-	90.74 %

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	8.0628	-1.204	-2.2136	3.9157	0.9527	4.5463	-0.1826	-0.4408	0.2217	0.5926	0.2625	0.108	-0.2491	-0.1872	-0.0799	0.5163	0.0125	-0.1701	0.2716	0.0096	0.4812	134.1312	23.4234	-35.3434
2	4.6011	0.3249	3.2688	10.2804	1.5753	2.5778	-0.0617	-0.2318	0.1386	1.122	0.1375	0.4498	0.1703	-0.1019	-0.0758	0.4841	0.0085	-0.1092	0.1655	-0.0657	0.6646	129.6946	24.7535	-38.5357
3	0.9947	1.7543	-1.4048	8.2697	1.1263	4.7813	0.0042	0.1271	0.1563	0.0924	-0.079	0.341	-0.2066	-0.3122	0.0748	0.4075	0.0012	-0.2067	0.1961	0.0129	0.481	126.5095	22.8879	-44.9757
4	4.0737	0.3227	0.8378	8.7365	-1.5469	5.2027	-0.1234	0.2459	0.391	-0.8085	0.094	0.007	-0.478	0.3611	0.0293	0.4433	-0.0521	-0.0539	0.3246	0.0345	0.5397	138.7942	21.5797	-51.8791
5	3.4897	0.6237	-0.308	6.5726	-2.5763	2.0242	-0.0848	-0.2552	0.3215	0.2246	0.0251	0.0123	-0.1149	0.2189	0.0597	0.4295	-0.0513	-0.1505	0.2433	-0.0063	0.4748	138.7143	19.9276	-42.6568
6	11.3046	-13.1849	11.9809	17.8083	-17.7131	18.5866	0.4741	0.0569	0.3875	-0.3097	-0.7856	-0.4404	0.3734	1.2919	0.3115	0.5539	0.0214	-0.192	0.4684	0.0543	0.6936	152.4315	15.3062	-44.9627
7	6.8568	-3.1289	3.8115	5.0795	-5.129	9.7531	-0.4675	-0.7344	0.4125	0.6986	-0.1442	-0.0394	-0.6748	0.3858	0.6117	0.3305	0.0086	-0.1657	0.404	-0.0165	0.5098	145.69	13.1185	-34.648
8	7.4382	4.0633	-3.1105	16.4167	-4.198	7.4074	-0.1503	0.5604	0.0707	-1.6109	-0.3154	-0.9262	0.5264	0.6189	0.4657	0.328	0.1041	-0.0645	0.2991	0.0026	0.478	146.1292	9.3547	-49.3219
9	19.161	-8.3036	-9.4338	7.9524	4.8153	4.7689	0.1525	0.8411	-1.5383	-1.943	-0.8942	0.7527	-0.3648	-0.5145	0.7417	1.2758	-0.2146	-0.1341	0.6138	-0.1762	0.553	145.8145	-13.1381	27.4952
10	4.9529	5.4442	1.0447	6.1009	1.0817	0.3056	0.2981	0.1743	0.3603	0.5736	-0.0989	0.6011	-0.0144	0.1078	-0.1991	0.736	-0.6062	0.1582	1.018	-0.2649	0.9701	130.5103	-9.1732	27.9096
11	38.8988	2.6733	17.7304	3.3335	-8.2449	36.5289	-1.1134	-2.1015	-0.8009	0.5242	1.2028	-0.1776	-2.3722	-4.975	-0.0894	0.6287	-0.1183	0.3793	1.1573	-0.2067	0.6042	133.702	-6.9015	36.7495
12	73.6391	5.4703	48.3185	0.6329	3.4703	31.7812	0.5872	-1.853	0.6672	-0.2115	-0.8019	0.3195	0.5873	-0.9186	0.2147	1.6966	0.4939	0.1656	2.1161	-0.5657	1.2725	125.8798	-12.7578	36.5062
13	9.8187	-1.1408	2.9055	9.4796	-2.6326	1.4465	0.5038	-1.1709	-1.4264	-0.3852	-0.1075	0.2119	0.3641	-0.3688	-0.3963	0.8088	-0.5194	0.1719	0.4286	0.019	0.2957	142.3112	-10.8123	41.1786
14	12.1239	3.7414	1.154	2.1562	3.6197	10.859	-0.2374	0.0768	-0.5459	0.1504	-0.3498	0.0964	0.545	-1.1632	0.5873	0.5753	-0.3646	0.1533	0.4649	0.0427	0.7311	144.5332	-4.3586	34.5236
15	9.4838	-0.5908	0.3876	11.0954	-0.7672	11.6346	-0.0681	0.824	-0.2648	-0.2642	-0.1292	-0.1576	0.9142	0.1717	0.1972	0.4014	-0.1684	-0.0077	0.4267	-0.0822	0.4688	152.5534	-1.1002	29.8585
16	17.1597	5.1528	3.1694	1.5776	1.0275	0.7763	0.2866	-1.4546	-0.7011	0.1869	-0.3575	-0.1361	0.3096	-0.0863	0.0709	1.0375	0.118	0.03	0.4684	0.1608	0.4122	156.5505	-3.8857	41.408
17	11.9299	-2.6421	-3.5541	3.9243	0.8038	4.6142	-0.1212	0.1488	-0.8035	0.0222	-0.1567	0.3891	0.348	-0.5599	0.2779	0.3015	-0.0239	-0.1043	0.5294	0.0502	0.4263	126.5102	1.6509	-12.563
18	8.2383	1.614	-5.8143	5.6041	-3.0721	16.5269	-0.061	-0.3347	0.2468	0.0903	-0.0815	-0.3195	0.3375	-0.8499	0.1425	0.3199	0.0842	-0.1014	0.6083	0.0784	0.6068	123.7063	4.416	-13.1341
19	7.5446	-4.6635	-2.918	10.6384	12.8245	31.0219	0.1146	-0.5977	0.129	0.2641	0.223	-0.1098	-0.6326	-1.1161	-0.3376	0.2452	-0.0608	-0.0148	0.524	0.0797	0.5013	124.2246	10.9964	-13.3356
20	19.6064	-5	-4.6167	12.9068	1.9118	1.1468	0.4526	1.6376	1.5721	1.4983	-0.1726	1.4407	0.0092	-0.4849	-0.28	0.5714	0.1879	-0.0183	1.2996	0.1888	0.7171	113.2557	14.5042	-10.1857
21	3.9117	-1.489	-0.0061	0.8309	-0.5088	4.6544	0.2034	-0.6744	0.3725	0.0232	0.0014	0.0186	-0.5904	0.5831	-0.2048	0.3121	-0.0746	-0.1044	0.6824	0.0487	0.6113	138.4787	11.3117	-16.5306
22	73.3684	-12.685	-7.1066	70.3441	10.3387	1.911	-1.5537	0.2089	2.152	-0.4223	1.4149	1.9906	0.0657	0.2156	0.1387	0.6666	0.2791	-0.1815	1.0925	0.2511	0.3802	138.8823	15.8331	-11.4722
23	3.8117	-0.1143	1.5996	0.9328	-1.5464	16.2588	0.0613	-0.2859	-0.0591	-0.0369	0.0483	0.0438	0.6063	0.0241	-0.1096	0.3746	0.0311	-0.0453	0.2994	0.0582	0.5115	136.1151	4.1221	-25.2194
24	19.0171	-9.5463	-4.5834	33.1941	5.9497	1.5889	0.0538	-1.7364	-0.0089	1.3118	0.0993	-0.8685	0.1941	0.2268	-0.153	0.3688	-0.1028	-0.1769	0.8702	0.1827	0.2911	144.773	1.8371	-5.1291
25	0.9512	-1.7388	0.4712	5.5987	2.5291	7.4301	-0.1765	-0.1391	0.0962	-0.8464	-0.1208	0.8954	-1.7843	-0.6117	0.2973	0.7517	-0.0808	-0.5635	0.5993	-0.0525	1.1476	126.0334	14.2117	11.6711
26	12.0275	-36.0875	20.6904	108.647	-62.021	35.6304	-1.4984	-1.4836	-1.8382	3.7834	4.5444	6.0182	-2.711	-2.2943	-3.046	1.9034	0.2193	-0.8194	2.5837	0.5618	1.0075	122.8797	13.5942	3.2195
27	11.8537	-10.2751	-11.0859	28.5529	8.2061	25.4321	-0.3007	-0.3195	0.072	0.5258	-0.4478	1.0557	-1.4006	-0.5278	0.7485	0.3473	-0.2252	-0.0621	0.7735	-0.097	0.5927	124.9392	9.1651	15.9346
28	7.2284	1.9313	-2.2021	8.1871	-1.2244	7.4277	-0.276	0.0861	0.3961	-1.0429	0.1189	1.5533	-0.3824	-1.0728	0.1571	0.2097	-0.0618	-0.2476	0.6983	0.0401	0.6426	119.203	4.6315	12.4298
29	3.6659	-4.2108	-0.0632	7.4855	-3.0763	8.3794	-0.1488	0.0714	-0.6338	0.365	0.544	-0.2195	0.6691	0.2815	-0.3952	0.3111	-0.0741	-0.4002	1.1165	-0.3979	1.0021	135.7645	3.3604	12.8897
30	25.7201	-24.2395	14.8088	23.6603	-20.3244	58.4465	-0.4449	0.8145	-0.6426	0.2238	-0.609	0.3733	1.0394	-0.6403	1.0539	0.517	0.0423	0.3441	0.9074	-0.1388	0.846	143.9976	2.7612	5.8617
31	4.7882	-1.8335	5.4265	0.9763	-0.423	19.5129	0.0664	0.1047	-0.0798	0.0031	0.0522	0.0687	-0.1981	-0.1921	-0.1187	0.2952	-0.1994	-0.0124	0.6915	0.0639	0.5122	139.4856	9.1931	19.4256
32	9.7562	9.788	-6.7563	10.6089	-7.9274	7.9504	-0.5343	0.5649	1.1613	-0.5467	0.3764	0.4886	-0.6132	-0.6887	0.1578	0.7271	0.1788	0.0017	0.6003	0.1528	0.7422	142.1145	13.959	-0.1544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 31
2	X-RAY DIFFRACTION	2	A	32 - 50
3	X-RAY DIFFRACTION	3	A	51 - 70
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18	X-RAY DIFFRACTION	18	C	348 - 362
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22	X-RAY DIFFRACTION	22	C	411 - 417
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