PDB-6wur: Crystal structure of PRL-2 phosphatase C101D mutant in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 6wur

Title

Crystal structure of PRL-2 phosphatase C101D mutant in complex with the Bateman domain of CNNM3 magnesium transporter

Components

Metal transporter CNNM3
Protein tyrosine phosphatase type IVA 2

Keywords

METAL TRANSPORT/HYDROLASE / phosphatase / magnesium transporter / protein binding / METAL TRANSPORT / METAL TRANSPORT-HYDROLASE complex

Function / homology

Function and homology information

: / magnesium ion homeostasis / intracellular manganese ion homeostasis / RAB geranylgeranylation / transmembrane transporter activity / monoatomic ion transport / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.882 Å

Authors

Kozlov, G. / Gehring, K.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of PRL phosphatase C104D mutant in complex with the Bateman domain of CNNM magnesium transporter
Authors: Kozlov, G. / Funato, Y. / Chen, S. / Zhang, Z. / Illes, K. / Miki, H. / Gehring, K.

History

Deposition	May 5, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6wur.cif.gz	136.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6wur.ent.gz	104.6 KB	Display	PDB format
PDBx/mmJSON format	6wur.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6wur_validation.pdf.gz	438.3 KB	Display	wwPDB validaton report
Full document	6wur_full_validation.pdf.gz	446.2 KB	Display
Data in XML	6wur_validation.xml.gz	13.7 KB	Display
Data in CIF	6wur_validation.cif.gz	17.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/6wur ftp://data.pdbj.org/pub/pdb/validation_reports/wu/6wur	HTTPS FTP

-
Related structure data

Related structure data	6wusC 5k22S 5vmi PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5k25-1 6wus-1 5tsr-d 5k23-1 5mmz-1 5k22-1 5lxq-d 4qpl-d 5k24-d 3e19-3 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (5) #126 - Jun 2010 Epidermal Growth Factor similarity (8) #140 - Aug 2011 Rhomboid Protease GlpG similarity (3) #225 - Sep 2018 Phytase similarity (3)

Deposited unit

A: Protein tyrosine phosphatase type IVA 2

B: Metal transporter CNNM3

hetero molecules

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

1

A: Protein tyrosine phosphatase type IVA 2

B: Metal transporter CNNM3

hetero molecules

A: Protein tyrosine phosphatase type IVA 2

B: Metal transporter CNNM3

hetero molecules

defined by author&software
Evidence: gel filtration
79.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.857, 124.544, 153.413
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Protein tyrosine phosphatase type IVA 2 / HU-PP-1 / OV-1 / PTP(CAAXII) / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of ...HU-PP-1 / OV-1 / PTP(CAAXII) / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of regenerating liver 2 / PRL-2 Mass: 21868.209 Da / Num. of mol.: 1 / Mutation: C101D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A2, PRL2, PTPCAAX2, BM-008 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12974, protein-tyrosine-phosphatase
#2: Protein	Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / Cyclin-M3 Mass: 17634.027 Da / Num. of mol.: 1 / Fragment: UNP Q8NE01 residues 309-452 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NE01
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.22 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.1 M sodium acetate, pH 5.1, 0.54 M sodium citrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6235 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2016
Radiation	Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6235 Å / Relative weight: 1
Reflection	Resolution: 2.88→50 Å / Num. obs: 11721 / % possible obs: 92.38 % / Redundancy: 2.9 % / R_sym value: 0.074 / Net I/σ(I): 13
Reflection shell	Resolution: 2.88→2.95 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1010 / R_sym value: 0.592 / % possible all: 80.93

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5K22

5k22

Resolution: 2.882→24.173 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.83

	R_factor	Num. reflection	% reflection
R_free	0.2949	605	5.16 %
R_work	0.2377	-	-
obs	0.2407	11721	92.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.882→24.173 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2237	0	1	4	2242

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2284
X-RAY DIFFRACTION	f_angle_d	0.75	3134
X-RAY DIFFRACTION	f_dihedral_angle_d	3.431	1354
X-RAY DIFFRACTION	f_chiral_restr	0.045	379
X-RAY DIFFRACTION	f_plane_restr	0.006	414

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 (%)
2.8823-3.1718	0.373	118	0.3631	2665	X-RAY DIFFRACTION	89
3.1718-3.6294	0.377	160	0.3033	2820	X-RAY DIFFRACTION	95
3.6294-4.5676	0.2996	171	0.2282	2817	X-RAY DIFFRACTION	95
4.5676-24.173	0.2607	156	0.2089	2814	X-RAY DIFFRACTION	90

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	0.2181	-0.074	-0.1181	0.1871	0.077	0.0267	1.0903	-0.9069	0.5105	-0.1871	-0.3248	-0.3181	-0.4268	0.5469	-0.0009	0.9559	-0.1043	-0.0564	1.193	-0.2146	1.4411	9.89	20.3677	181.3476
2	1.0587	0.2788	0.7812	0.4518	-0.0406	0.8523	0.2483	-0.6665	0.0281	-0.366	0.2736	-1.4096	0.4767	0.8241	0.2946	0.869	0.2871	0.3242	0.8521	0.0695	0.7813	9.904	33.8117	179.1824
3	0.4668	-0.036	0.0888	0.1913	-0.0931	0.0585	-0.2508	-0.5959	-1.1391	-0.0474	1.4566	-0.7097	0.8403	1.3347	-0.0165	1.1375	0.2189	-0.073	1.3263	-0.3085	1.038	15.0853	33.1806	186.9228
4	1.0584	-0.1634	0.1689	1.1835	-1.6257	2.2834	-1.6187	-1.2883	-0.1589	0.8859	1.8729	0.014	-0.5816	-0.7211	0.0739	0.8822	0.1408	0.1494	1.0485	-0.1315	1.0095	3.7609	34.2246	186.5368
5	0.5822	-0.7438	0.2063	0.882	-0.026	1.0876	-0.4973	-1.5902	-0.3918	0.204	0.2998	-0.1844	0.059	-0.4892	0.0041	1.1134	0.358	-0.2253	1.127	-0.2625	1.1175	0.1733	35.7992	186.0415
6	0.0677	-0.0842	-0.1519	0.141	0.1896	0.5191	0.8109	-0.6852	0.0277	0.1669	-0.177	-0.2045	-0.8125	0.522	0.0256	1.2077	0.3878	-0.1802	1.1844	-0.1236	0.8782	-0.9856	45.1412	178.1294
7	3.2096	2.0899	-1.1052	3.6851	-1.4803	1.1097	-0.4498	0.3305	-1.267	-1.1771	-0.6585	-1.2374	-0.3337	-0.5622	-0.2299	0.8098	0.168	0.0007	0.9521	-0.2343	0.8637	3.6309	35.938	175.5291
8	2.3062	1.547	0.6408	2.0562	-0.3318	0.7617	0.4555	1.395	-0.0043	-1.0731	0.4526	-0.4406	-0.7767	0.0216	3.0535	1.7899	0.3339	0.1313	1.1148	-0.107	0.5967	5.3608	33.0731	163.9282
9	0.2169	0.14	-0.1573	0.4742	-0.0346	0.0965	-1.3276	1.3839	-0.1719	-0.8268	0.2951	-0.2221	-0.9056	-0.4515	-0.0136	1.2738	0.234	0.0167	1.2789	-0.175	1.0586	-2.2909	27.9161	168.8788
10	1.332	0.1896	1.0134	3.2679	-0.2248	3.8195	-0.123	0.8844	0.0108	-0.2531	-0.3392	0.3931	0.0904	0.9631	-2.7341	1.8544	0.9403	-0.4968	1.2418	-0.0463	0.4304	-5.5718	42.963	165.8915
11	0.1871	0.0626	-0.2345	0.3858	-0.2961	0.3626	0.0355	0.3084	-1.1831	-1.5463	-0.3714	1.8535	-0.0791	-0.9272	-0.0027	0.8941	0.0081	0.0974	0.6742	-0.0495	0.8351	23.6858	-0.9936	158.8151
12	1.9993	-0.9877	-0.226	0.4465	0.0794	0.6433	0.1538	-0.0702	-0.9708	-0.2222	-0.3983	1.1457	1.0354	-0.9596	-0.0473	1.2002	-0.0484	0.0832	0.7226	-0.1005	0.8914	13.2218	4.2012	182.1492
13	0.4011	-0.174	0.0223	0.2555	-0.0921	0.0987	0.022	0.0027	0.4255	1.0196	-0.89	-0.5004	0.2431	-0.5646	0.0052	0.6958	-0.0121	0.0605	0.8582	0.0676	1.0674	21.6229	-2.3631	195.5183
14	1.4329	-0.5417	0.2816	1.3853	0.2027	0.4902	0.0131	0.3296	-0.1893	0.7157	-0.0995	-0.2904	-0.3263	-0.0864	-0.0018	0.8285	0.0054	0.0112	0.7904	-0.0574	0.845	20.0995	8.0975	192.5978
15	0.3327	-0.434	-0.3447	0.8199	0.3925	0.1572	0.2539	-0.0906	0.0043	-0.0055	-0.0848	0.1674	-1.0363	-0.2227	0.0019	1.1479	0.0472	-0.0334	0.7175	-0.0514	0.9327	20.7817	13.1866	179.5439
16	1.6062	-1.5164	-0.6016	5.1795	-4.3453	7.1236	0.5812	0.0204	-0.9122	-0.1174	0.6853	0.1653	-1.0412	0.2698	2.363	0.8174	-0.3814	-0.1374	0.7484	-0.5781	0.3131	16.0359	12.3935	176.0313
17	1.2672	0.7968	0.4612	1.3506	0.0428	0.2285	0.7597	0.1308	-0.041	-0.1641	1.1199	0.8679	0.2893	0.9355	0.0088	1.0949	0.2954	-0.1194	1.0894	-0.4225	1.3978	-4.0646	19.7926	173.9537
18	0.6662	0.3703	-0.0359	0.6777	-0.0859	0.0473	-0.1436	-0.6473	-0.2023	0.2552	0.104	0.6721	-0.2827	0.1233	0.0316	0.5583	0.0936	-0.1362	0.7791	-0.0729	0.8311	16.3307	4.5514	173.0574

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 6 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 7 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 37 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 38 through 51 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 52 through 74 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 91 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 92 through 118 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 119 through 133 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 134 through 147 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 148 through 154 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 298 through 310 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 311 through 334 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 335 through 344 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 345 through 378 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 379 through 407 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 408 through 420 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 421 through 427 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 428 through 446 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi