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- PDB-5k23: Crystal structure of the complex between human phosphatase PRL-2 ... -

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Basic information

Entry
Database: PDB / ID: 5k23
TitleCrystal structure of the complex between human phosphatase PRL-2 in the oxidized state with the Bateman domain of human magnesium transporter CNNM3
Components
  • Metal transporter CNNM3
  • Protein tyrosine phosphatase type IVA 2
KeywordsHYDROLASE/TRANSPORTER PROTEIN/PROTEIN BINDING / Complex / phosphatase / magnesium transporter / protein binding / HYDROLASE / HYDROLASE-TRANSPORTER PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


magnesium ion homeostasis / RAB geranylgeranylation / transmembrane transporter activity / enzyme inhibitor activity / monoatomic ion transport / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome / nucleus / membrane ...magnesium ion homeostasis / RAB geranylgeranylation / transmembrane transporter activity / enzyme inhibitor activity / monoatomic ion transport / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / CBS domain superfamily ...Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 2 / Metal transporter CNNM3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsGulerez, I. / Kozlov, G. / Gehring, K.
CitationJournal: Sci Rep / Year: 2017
Title: PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3.
Authors: Zhang, H. / Kozlov, G. / Li, X. / Wu, H. / Gulerez, I. / Gehring, K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)39,4902
Polymers39,4902
Non-polymers00
Water00
1
A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3

A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)78,9814
Polymers78,9814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5530 Å2
ΔGint-48 kcal/mol
Surface area28020 Å2
MethodPISA
2
A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3

A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3

A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3

A: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)157,9618
Polymers157,9618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12510 Å2
ΔGint-111 kcal/mol
Surface area54600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.156, 124.490, 159.048
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 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: 21856.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A2, PRL2, PTPCAAX2, BM-008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.54M sodium citrate, 0.1M sodium acetate, 10mM yttrium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2012
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 10491 / % possible obs: 99.51 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.047 / Net I/σ(I): 33.2
Reflection shellResolution: 2.96→3.04 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.3 / % possible all: 94.06

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZCK

1zck


Resolution: 2.96→49.02 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.731 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.023 / ESU R Free: 0.38 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26365 528 4.8 %RANDOM
Rwork0.20499 ---
obs0.20786 10440 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.237 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.96→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 0 0 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9753323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2735301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.40424.071113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.72515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1191517
X-RAY DIFFRACTIONr_chiral_restr0.1190.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.959→3.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 37 -
Rwork0.287 644 -
obs--94.06 %

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