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- PDB-5mmz: Structure of PRL-1 in complex with the Bateman domain of CNNM2 -

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Basic information

Entry
Database: PDB / ID: 5mmz
TitleStructure of PRL-1 in complex with the Bateman domain of CNNM2
Components
  • Metal transporter CNNM2
  • Protein tyrosine phosphatase type IVA 1
KeywordsMETAL TRANSPORT / Cyclin M / Magnesium transport / ACDP
Function / homology
Function and homology information


prenylated protein tyrosine phosphatase activity / magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle ...prenylated protein tyrosine phosphatase activity / magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / basolateral plasma membrane / early endosome / endosome / positive regulation of cell migration / cell cycle / 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: 2.4 Å
AuthorsGimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. ...Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / Claverie-Martin, F. / Muller, D. / Tremblay, M.L. / Martinez-Cruz, L.A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.
Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / ...Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / Claverie-Martin, F. / Muller, D. / Tremblay, M.L. / Martinez-Cruz, L.A.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Dec 20, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 17, 2024Group: 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)37,7112
Polymers37,7112
Non-polymers00
Water1267
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)75,4234
Polymers75,4234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-x+3,-y+2,z1
Unit cell
Length a, b, c (Å)52.730, 128.478, 153.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 17866.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm2, Acdp2 / 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: 19845.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptp4a1, Prl1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63739, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2M Sodium Formate, 0.1M Sodium Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9723 Å / Relative weight: 1
ReflectionResolution: 2.4→98.63 Å / Num. obs: 20944 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.99 / Rsym value: 0.054 / Net I/σ(I): 26.5
Reflection shellResolution: 2.4→2.41 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.86 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IY0

4iy0


Resolution: 2.4→98.6 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.99
RfactorNum. reflection% reflection
Rfree0.2519 1019 4.87 %
Rwork0.2254 --
obs0.2266 20921 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→98.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 0 7 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032348
X-RAY DIFFRACTIONf_angle_d0.8043191
X-RAY DIFFRACTIONf_dihedral_angle_d10.311839
X-RAY DIFFRACTIONf_chiral_restr0.029372
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.398-2.52440.37691360.33622775X-RAY DIFFRACTION99
2.5244-2.68260.3081390.29052782X-RAY DIFFRACTION100
2.6826-2.88960.34631620.2922806X-RAY DIFFRACTION100
2.8896-3.18030.31661570.28162810X-RAY DIFFRACTION100
3.1803-3.64030.25691380.24012841X-RAY DIFFRACTION100
3.6403-4.58540.24111410.20842878X-RAY DIFFRACTION100
4.5854-41.20690.2081460.1953010X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 62.0706 Å / Origin y: 150.2689 Å / Origin z: 180.7528 Å
111213212223313233
T0.5012 Å2-0.027 Å20.0319 Å2-0.5442 Å2-0.085 Å2--0.5408 Å2
L1.346 °2-1.3004 °20.1173 °2-2.7744 °2-0.1168 °2--0.6182 °2
S0.0716 Å °-0.0658 Å °0.1819 Å °-0.0101 Å °-0.1051 Å °-0.0369 Å °-0.2911 Å °-0.1517 Å °0.0107 Å °
Refinement TLS groupSelection details: all

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