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

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Basic information

Entry
Database: PDB / ID: 5lxq
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


: / 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 / spindle / basolateral plasma membrane ...: / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / Metal transporter CNNM2 / Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.335 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. / 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
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Database references
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Jan 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
B: Protein tyrosine phosphatase type IVA 1
A: Metal transporter CNNM2
C: Protein tyrosine phosphatase type IVA 1
H: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1728
Polymers81,0274
Non-polymers1,1454
Water00
1
B: Protein tyrosine phosphatase type IVA 1
A: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0864
Polymers40,5142
Non-polymers5732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein tyrosine phosphatase type IVA 1
H: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0864
Polymers40,5142
Non-polymers5732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.930, 125.560, 61.040
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein tyrosine phosphatase type IVA 1 / Protein-tyrosine phosphatase 4a1 / Protein-tyrosine phosphatase of regenerating liver 1 / PRL-1


Mass: 22647.260 Da / Num. of mol.: 2
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
#2: Protein Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / mACDP2 / Cyclin-M2


Mass: 17866.381 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M Sodium formate, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2837 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
ReflectionResolution: 3.1→97.64 Å / Num. obs: 10602 / % possible obs: 99.16 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16
Reflection shellResolution: 3.331→3.342 Å / Rmerge(I) obs: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IY0 and 1ZCK

4iy0

1zck


Resolution: 3.335→47.882 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1540 10.06 %
Rwork0.2027 --
obs0.2056 15312 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.335→47.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 64 0 4712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144819
X-RAY DIFFRACTIONf_angle_d1.6766557
X-RAY DIFFRACTIONf_dihedral_angle_d11.8331758
X-RAY DIFFRACTIONf_chiral_restr0.058756
X-RAY DIFFRACTIONf_plane_restr0.01862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3349-3.44250.268570.2933483X-RAY DIFFRACTION34
3.4425-3.56550.3222960.2616880X-RAY DIFFRACTION63
3.5655-3.70820.31151350.26151211X-RAY DIFFRACTION88
3.7082-3.87690.29831570.25061422X-RAY DIFFRACTION100
3.8769-4.08120.25911520.22791382X-RAY DIFFRACTION100
4.0812-4.33670.19611600.19071396X-RAY DIFFRACTION100
4.3367-4.67130.20821540.1641402X-RAY DIFFRACTION100
4.6713-5.14090.21921540.16761372X-RAY DIFFRACTION100
5.1409-5.88360.22021590.19931426X-RAY DIFFRACTION100
5.8836-7.40830.26221560.21911394X-RAY DIFFRACTION100
7.4083-47.88710.17991600.17821404X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 481.594 Å / Origin y: -57.3341 Å / Origin z: 123.6086 Å
111213212223313233
T0.358 Å2-0.0274 Å20.0593 Å2-0.3981 Å20.0934 Å2--0.3307 Å2
L0.6526 °2-0.366 °2-0.0158 °2-1.8945 °20.7644 °2--0.6782 °2
S0.1001 Å °-0.0294 Å °-0.0057 Å °-0.0242 Å °-0.1604 Å °0.0446 Å °0.0049 Å °0.0369 Å °-0.0055 Å °
Refinement TLS groupSelection details: all

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