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- PDB-6wus: Crystal structure of PRL-1 phosphatase C104D mutant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6wus
TitleCrystal structure of PRL-1 phosphatase C104D mutant in complex with the Bateman domain of CNNM2 magnesium transporter
Components
  • Metal transporter CNNM2
  • Protein tyrosine phosphatase type IVA 1
KeywordsMETAL TRANSPORT/HYDROLASE / phosphatase / magnesium transporter / protein binding / METAL TRANSPORT / METAL TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


: / magnesium ion transport / magnesium ion homeostasis / protein tyrosine/serine/threonine phosphatase activity / magnesium ion transmembrane transporter activity / cell cycle / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle ...: / magnesium ion transport / magnesium ion homeostasis / protein tyrosine/serine/threonine phosphatase activity / magnesium ion transmembrane transporter activity / cell cycle / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle / basolateral plasma membrane / early endosome / endosome / positive regulation of cell migration / glutamatergic synapse / synapse / endoplasmic reticulum / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain ...Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / RmlC-like jelly roll fold / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Metal transporter CNNM2 / Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.758 Å
AuthorsKozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RPGIN2014-04686 Canada
CitationJournal: 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
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM2
B: Protein tyrosine phosphatase type IVA 1


Theoretical massNumber of molelcules
Total (without water)36,2222
Polymers36,2222
Non-polymers00
Water1629
1
A: Metal transporter CNNM2
B: Protein tyrosine phosphatase type IVA 1

A: Metal transporter CNNM2
B: Protein tyrosine phosphatase type IVA 1


Theoretical massNumber of molelcules
Total (without water)72,4434
Polymers72,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_325-x-2,-y-3,z1
Unit cell
Length a, b, c (Å)52.138, 127.935, 152.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

#1: Protein Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / mACDP2 / Cyclin-M2


Mass: 17408.793 Da / Num. of mol.: 1 / Fragment: UNP residues 430-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm2, Acdp2 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TWN3
#2: Protein Protein tyrosine phosphatase type IVA 1 / Protein-tyrosine phosphatase 4a1 / Protein-tyrosine phosphatase of regenerating liver 1 / PRL-1


Mass: 18812.768 Da / Num. of mol.: 1 / Mutation: C104D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptp4a1, Prl1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q63739, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 0.1 M sodium acetate, pH 5.3, 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2017
RadiationMonochromator: Single-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 12756 / % possible obs: 94.08 % / Redundancy: 5 % / Rsym value: 0.069 / Net I/σ(I): 24.6
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 648 / Rsym value: 0.549 / % possible all: 88.96

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5MMZ

5mmz


Resolution: 2.758→41.063 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.91
RfactorNum. reflection% reflection
Rfree0.2809 662 5.19 %
Rwork0.2404 --
obs0.2426 12756 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.758→41.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 0 9 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062353
X-RAY DIFFRACTIONf_angle_d0.8243203
X-RAY DIFFRACTIONf_dihedral_angle_d5.9861410
X-RAY DIFFRACTIONf_chiral_restr0.048375
X-RAY DIFFRACTIONf_plane_restr0.006416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.758-2.97060.3781330.30732316X-RAY DIFFRACTION92
2.9706-3.26940.41161310.3092437X-RAY DIFFRACTION97
3.2694-3.74220.30161240.26272446X-RAY DIFFRACTION96
3.7422-4.71370.28081390.21262438X-RAY DIFFRACTION95
4.7137-41.0630.22911350.22422457X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.0186-1.71741.75050.3573-0.45180.8092-0.8648-0.14771.66840.82340.0326-0.863-0.86181.3544-0.38721.06090.10640.07980.93850.13690.3348-47.8567-189.9671309.7847
20.3666-0.5329-0.01281.40050.41173.16990.8048-0.1960.80150.24640.2893-1.47020.01741.0541.12110.4911-0.1294-0.12270.56560.14220.5313-36.6968-196.2474333.1118
30.4007-0.3050.03740.3263-0.06030.16370.1689-0.05650.39380.5798-0.353-0.39230.32260.2514-0.01540.8227-0.3102-0.10580.71010.11990.6086-44.9374-189.7819348.9083
42.4712-1.504-0.20311.89670.78120.52870.410.78340.50550.3948-0.6119-1.45670.12350.49030.14670.082-0.0926-0.56590.71740.22970.2738-38.2744-198.4024338.732
50.36310.15120.45310.574-0.0740.6426-0.13790.46360.20240.264-0.0698-0.6170.8289-0.75690.00250.57550.0239-0.10780.4752-0.06750.4499-46.4663-201.0484340.7812
62.0591.69840.78221.71730.94440.62490.8691-0.8027-0.12711.0726-1.10130.05390.92940.00420.03260.7207-0.2136-0.13460.80620.28680.4787-49.2631-198.6594355.3198
70.5643-0.372-0.14480.9390.31250.10620.3596-0.3924-0.82710.22440.1584-0.40451.0809-1.3230.03920.5737-0.27330.2370.6352-0.03890.6076-46.7048-206.4337343.6889
80.37941.22450.47734.29291.80720.7378-0.14080.46580.24640.2405-0.3009-1.30070.37880.11140.31540.40250.16790.15930.71950.21030.5712-38.0987-205.7855321.857
91.2997-0.82610.19810.50310.00391.42710.5461-0.1173-0.4245-0.1494-0.4958-1.2725-0.2371-0.2419-0.08570.3482-0.00280.11180.38330.13421.0426-38.0996-205.8503324.0116
101.87760.02721.30013.1338-0.26662.0077-0.3153-0.56041.0097-0.1956-0.079-1.7571-0.0329-0.2624-0.00550.38240.03620.01870.5022-0.00680.4311-41.063-195.9008323.5894
114.4442-2.3761-0.61754.6736-1.3432.93810.1422-0.5466-0.74481.17531.52712.24530.2803-2.00041.10130.76810.43560.14740.32410.01630.7874-36.0365-226.4541334.0784
120.1244-0.3184-0.53734.5511-0.00753.1806-0.322-0.090.6232.13990.9747-1.90381.5363-0.37520.28721.46730.18150.0010.89620.21021.2489-25.3532-227.4872339.0034
134.899-2.63622.12985.20311.65212.9780.1917-0.5124-0.1115-0.56240.0512-0.20330.4720.53650.02560.60920.2552-0.07010.54960.1650.5407-27.3544-233.3215328.1118
143.36882.7416-0.86563.02580.05891.67130.718-0.2750.8034-2.6348-0.8103-0.0320.5370.22-0.83541.44040.39820.30310.63580.19080.5314-25.665-224.7732317.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 429 through 442 )
2X-RAY DIFFRACTION2chain 'A' and (resid 443 through 466 )
3X-RAY DIFFRACTION3chain 'A' and (resid 467 through 475 )
4X-RAY DIFFRACTION4chain 'A' and (resid 476 through 490 )
5X-RAY DIFFRACTION5chain 'A' and (resid 491 through 500 )
6X-RAY DIFFRACTION6chain 'A' and (resid 501 through 510 )
7X-RAY DIFFRACTION7chain 'A' and (resid 511 through 522 )
8X-RAY DIFFRACTION8chain 'A' and (resid 523 through 530 )
9X-RAY DIFFRACTION9chain 'A' and (resid 531 through 560 )
10X-RAY DIFFRACTION10chain 'A' and (resid 561 through 578 )
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 47 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 157 )

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