PDB-8ct8: Crystal structure of Drosophila melanogaster PRL/CBS-pair domain ...

ID or keywords:

Entry

Database: PDB / ID: 8ct8

Title

Crystal structure of Drosophila melanogaster PRL/CBS-pair domain complex

Components

PRL-1 phosphatase
Unextended protein

Keywords

PROTEIN BINDING / PRL / CBS-pair / CNNM / transporter protein / complex / UEX

Function / homology

Function and homology information

cellular response to carbon dioxide / protein tyrosine/serine/threonine phosphatase activity / magnesium ion homeostasis / magnesium ion transmembrane transport / intracellular monoatomic ion homeostasis / magnesium ion transmembrane transporter activity / apicolateral plasma membrane / export across plasma membrane / negative regulation of BMP signaling pathway / transmembrane transporter activity ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Fakih, R. / Goldstein, R.H. / Kozlov, G. / Gehring, K.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Burst kinetics and CNNM binding are evolutionarily conserved properties of phosphatases of regenerating liver.
Authors: Fakih, R. / Goldstein, R.H. / Kozlov, G. / Gehring, K.

History

Deposition	May 13, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Apr 5, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ct8.cif.gz	258.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ct8.ent.gz	209.6 KB	Display	PDB format
PDBx/mmJSON format	8ct8.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/ct/8ct8 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ct8	HTTPS FTP

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Related structure data

Related structure data	5k22S S: Starting model for refinement
Similar structure data	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	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3) #48 - Dec 2003 Catabolite Activator Protein similarity (3) #145 - Jan 2012 Messenger RNA Capping similarity (5) #251 - Nov 2020 Adenylyl Cyclase similarity (3) #140 - Aug 2011 Rhomboid Protease GlpG similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (4) #225 - Sep 2018 Phytase similarity (3)

Deposited unit

A: Unextended protein

B: Unextended protein

C: PRL-1 phosphatase

D: PRL-1 phosphatase

hetero molecules

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

1

A: Unextended protein

C: PRL-1 phosphatase

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry, gel filtration
36.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Unextended protein

D: PRL-1 phosphatase

hetero molecules

defined by author&software
36.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.311, 83.311, 238.188
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	Unextended protein / Putative metal transporter uex Mass: 18183.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: uex, 41Ad, GroupIII, l(2)41Ad, CG42595 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B7P9G0
#2: Protein	PRL-1 phosphatase / Phosphatase of regenerating liver-1 Mass: 18455.309 Da / Num. of mol.: 2 / Mutation: C104A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PRL-1, BG:DS07473.3, PRL, CG4993 / Production host: Escherichia coli (E. coli) / References: UniProt: O61722, protein-tyrosine-phosphatase
#3: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.38 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane pH 6.5, 17% (wt/vol) PEG3350, 0.2 M NaI

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.95374 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95374 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.44 Å / Num. obs: 54823 / % possible obs: 99.72 % / Redundancy: 1.8 % / B_iso Wilson estimate: 50.44 Å² / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.04196 / R_pim(I) all: 0.04196 / R_rim(I) all: 0.05934 / Net I/σ(I): 20.04
Reflection shell	Resolution: 2.5→2.589 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.2839 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 5524 / CC_1/2: 0.855 / CC star: 0.96 / R_pim(I) all: 0.2839 / R_rim(I) all: 0.4015 / % possible all: 99.52

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.20_4459	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5K22

5k22

Resolution: 2.5→48.44 Å / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.275	3642	6.64 %
R_work	0.2253	-	-
obs	0.2285	54823	98.97 %

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→48.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4760	0	3	54	4817

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.432
X-RAY DIFFRACTION	f_dihedral_angle_d	12.525	1763
X-RAY DIFFRACTION	f_chiral_restr	0.038	780
X-RAY DIFFRACTION	f_plane_restr	0.003	867

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.53					X-RAY DIFFRACTION
2.53-2.57					X-RAY DIFFRACTION
2.57-2.6					X-RAY DIFFRACTION
2.6-2.64	0.3168	136	0.2765	1883	X-RAY DIFFRACTION	97
2.64-2.68	0.3311	138	0.2616	1976	X-RAY DIFFRACTION	98
2.68-2.73	0.2821	135	0.2667	1945	X-RAY DIFFRACTION	99
2.73-2.78	0.309	145	0.2585	1993	X-RAY DIFFRACTION	98
2.78-2.83	0.3168	140	0.2679	1913	X-RAY DIFFRACTION	99
2.83-2.88	0.3794	141	0.307	1992	X-RAY DIFFRACTION	99
2.88-2.94	0.3515	140	0.2855	1939	X-RAY DIFFRACTION	99
2.94-3	0.3559	137	0.2726	1992	X-RAY DIFFRACTION	99
3-3.07	0.3005	141	0.2561	1972	X-RAY DIFFRACTION	99
3.07-3.15	0.3126	141	0.2559	1957	X-RAY DIFFRACTION	99
3.15-3.23	0.2926	140	0.2465	1969	X-RAY DIFFRACTION	99
3.23-3.33	0.2867	141	0.2311	2012	X-RAY DIFFRACTION	99
3.33-3.44	0.3064	135	0.237	1949	X-RAY DIFFRACTION	99
3.44-3.56	0.2536	142	0.2486	2001	X-RAY DIFFRACTION	100
3.56-3.7	0.2748	139	0.2161	1964	X-RAY DIFFRACTION	100
3.7-3.87	0.3009	143	0.2085	2006	X-RAY DIFFRACTION	100
3.87-4.08	0.2783	137	0.189	1975	X-RAY DIFFRACTION	100
4.08-4.33	0.2727	143	0.1789	2007	X-RAY DIFFRACTION	100
4.33-4.66	0.24	139	0.1932	1989	X-RAY DIFFRACTION	100
4.66-5.13	0.2204	140	0.2095	1978	X-RAY DIFFRACTION	100
5.13-5.87	0.2633	145	0.2346	1991	X-RAY DIFFRACTION	100
5.88-7.4	0.2395	143	0.2298	1983	X-RAY DIFFRACTION	100
7.4-48.44	0.2093	137	0.1798	1968	X-RAY DIFFRACTION	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	3.3397	4.0312	1.5806	8.5833	0.2279	3.8538	0.3392	-0.2647	0.3763	0.61	-0.0817	0.8894	0.1144	-0.5564	-0.2147	0.4504	-0.0458	0.0297	0.3779	0.0001	0.4689	1.3521	27.3958	42.992
2	1.3174	0.8294	2.8114	3.5865	3.8788	9.311	-0.2126	0.2897	0.6655	-0.7091	-0.0642	0.2821	-1.813	-0.4352	0.228	0.7168	-0.1517	0.0667	0.4725	-0.0612	0.4916	20.7301	44.9572	53.5761
3	2.7276	1.2019	0.9002	2.606	2.136	4.3478	0.0927	0.0873	-0.0261	-0.0854	0.1481	-0.1867	-0.0143	0.4394	-0.1997	0.5252	-0.0818	0.0002	0.3798	-0.0453	0.417	18.6488	32.1883	46.2499
4	5.2601	0.7603	-2.5749	1.7102	0.6763	2.6254	0.6122	0.0707	0.773	0.0517	0.0184	0.0866	-0.4716	-0.1566	-0.7626	0.5698	-0.0384	-0.0125	0.304	0.015	0.5424	9.1903	31.3021	38.2389
5	0.4859	0.7465	0.2715	6.388	2.1265	2.3517	-0.2809	0.146	0.0277	-0.8622	0.3495	0.461	0.331	-0.5578	-0.0287	0.5563	-0.1738	-0.0649	0.6072	0.0421	0.43	11.9906	40.9331	70.6771
6	9.2002	0.2675	5.605	4.2964	2.4354	5.179	0.7275	-0.543	1.0821	0.1481	-1.0942	2.1987	1.2637	-0.5721	0.2456	0.9244	-0.3709	-0.1235	0.5751	0.0691	0.6753	5.4436	22.1117	57.658
7	1.6435	-0.0517	-0.2225	4.928	0.9845	5.5102	0.2338	-0.3405	-0.3644	-0.111	0.1577	0.299	1.2316	-1.1626	-0.3848	0.5816	-0.2843	-0.0765	0.6069	0.0227	0.471	13.377	26.8728	67.066
8	1.7428	-0.501	0.4896	5.9434	3.3522	5.6973	-0.1591	0.1372	-0.3317	0.0408	0.5562	-0.04	1.0285	0.4949	-0.2558	0.5935	-0.128	-0.0238	0.3513	0.0542	0.427	18.2874	24.3405	66.2449
9	1.9054	-0.7305	0.5905	6.7011	-3.6475	5.7483	-0.1711	-0.1898	-0.0547	0.0201	0.3845	0.3625	-0.1039	-0.6852	-0.2529	0.3211	-0.0136	-0.072	0.4958	-0.0387	0.4457	16.7803	39.0054	75.8429
10	3.1932	-3.892	-3.3789	9.189	5.4031	3.9367	-0.2103	-0.3872	0.1035	0.944	-0.2295	0.1638	-0.1352	-0.0641	0.1957	0.7572	-0.0882	0.0219	0.5059	-0.0949	0.632	26.3171	13.4947	27.1806
11	2.1001	-0.6603	1.5903	3.1063	1.6227	6.2027	0.008	-0.527	0.1872	0.869	0.141	-0.2704	0.1683	-0.3844	-0.2146	0.5099	-0.0299	-0.1146	0.5627	-0.0792	0.4869	30.7739	22.2496	37.258
12	7.0295	2.5063	0.0126	6.4602	3.7183	5.3268	0.1204	0.0651	0.5179	0.9702	0.3506	-1.8398	-0.2429	0.8513	-0.5356	0.611	-0.0738	-0.0945	0.6028	-0.1063	0.7644	37.3098	26.2168	32.6321
13	5.5612	-1.9097	2.9093	5.2489	-2.9041	9.2006	-0.4633	-0.0386	1.0127	0.303	-0.0361	-1.2952	-0.7015	1.1179	0.3628	0.4198	-0.095	0.0308	0.6485	-0.1034	0.8117	37.7983	26.8969	28.3366
14	4.9957	-0.7984	0.3599	5.1722	0.4488	7.2982	0.1009	0.1152	0.1715	0.3508	0.0181	-0.8235	0.6429	0.9216	-0.102	0.42	0.0646	-0.0157	0.4645	-0.0833	0.5092	34.946	18.2865	22.7978
15	2.1616	-2.0687	-0.5779	5.7999	1.4612	2.4316	0.1358	0.1293	0.004	-0.197	-0.3809	0.072	-0.1346	-0.0195	0.2331	0.445	-0.0176	0.0091	0.2597	-0.0486	0.4478	21.621	21.4375	18.0078
16	5.414	2.1907	-0.3792	8.5081	-2.477	2.4444	-0.2513	0.0921	-0.7418	0.0196	0.5134	-0.6012	0.5191	0.778	-0.306	0.5791	0.146	0.0966	0.4559	-0.1063	0.5064	33.6301	15.0811	11.2241
17	2.1105	0.2671	0.5858	3.3064	2.036	6.0954	0.1257	0.2728	0.083	-0.4606	-0.1516	0.0251	0.2204	0.3944	0.0566	0.6717	0.2099	0.0102	0.7421	-0.0501	0.6152	33.5912	27.1363	80.1792
18	5.2888	-0.624	0.3354	2.1753	-0.3676	3.3491	-0.3355	-0.5259	-0.2838	0.2842	0.2535	-0.3235	0.9647	0.8217	0.0393	0.6691	0.3256	-0.0522	0.6966	0.0254	0.6772	34.4757	24.3289	91.903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 358 through 387 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 388 through 406 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 407 through 483 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 484 through 512 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 357 through 396 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 397 through 404 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 405 through 430 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 431 through 460 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 461 through 511 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 13 through 21 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 22 through 45 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 46 through 60 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 61 through 82 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 83 through 127 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 128 through 154 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 155 through 165 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 13 through 44 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 45 through 165 )

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