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- PDB-5tsr: Crystal structure of PRL-3 phosphatase in complex with the Batema... -

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Basic information

Entry
Database: PDB / ID: 5tsr
TitleCrystal structure of PRL-3 phosphatase in complex with the Bateman domain of CNNM3 magnesium transporter
Components
  • Metal transporter CNNM3
  • Protein tyrosine phosphatase type IVA 3
KeywordsMETAL TRANSPORT / phosphatase / magnesium transporter / protein binding
Function / homology
Function and homology information


regulation of vascular endothelial growth factor signaling pathway / positive regulation of establishment of protein localization / magnesium ion homeostasis / positive regulation of vascular permeability / transmembrane transporter activity / endothelial cell migration / monoatomic ion transport / Notch signaling pathway / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase ...regulation of vascular endothelial growth factor signaling pathway / positive regulation of establishment of protein localization / magnesium ion homeostasis / positive regulation of vascular permeability / transmembrane transporter activity / endothelial cell migration / monoatomic ion transport / Notch signaling pathway / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to leukemia inhibitory factor / positive regulation of non-canonical NF-kappaB signal transduction / early endosome / regulation of DNA-templated transcription / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Polymorphic toxin system, DSP-PTPase phosphatase / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain ...Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Polymorphic toxin system, DSP-PTPase phosphatase / 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 / 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 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 3 / Metal transporter CNNM3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.188 Å
AuthorsKozlov, G. / Zhang, H. / 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
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 3
B: Metal transporter CNNM3
C: Protein tyrosine phosphatase type IVA 3
D: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)74,0294
Polymers74,0294
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-32 kcal/mol
Surface area27820 Å2
Unit cell
Length a, b, c (Å)155.339, 125.146, 52.042
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein tyrosine phosphatase type IVA 3 / PRL-R / Protein-tyrosine phosphatase 4a3 / Protein-tyrosine phosphatase of regenerating liver 3 / PRL-3


Mass: 19380.494 Da / Num. of mol.: 2 / Mutation: C104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A3, PRL3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O75365, protein-tyrosine-phosphatase
#2: Protein Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / Cyclin-M3


Mass: 17634.027 Da / Num. of mol.: 2
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) / Strain (production host): BL21 / References: UniProt: Q8NE01
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 0.064 M Tri-Na Citrate, 15% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.188→50 Å / Num. obs: 15609 / % possible obs: 96.6 % / Redundancy: 3.3 % / Rsym value: 0.106 / Net I/σ(I): 10.5
Reflection shellResolution: 3.188→3.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 1.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K22

5k22


Resolution: 3.188→27.738 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 32.86
RfactorNum. reflection% reflection
Rfree0.2871 805 5.16 %
Rwork0.2388 --
obs0.2413 15609 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.188→27.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 0 3 4767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094863
X-RAY DIFFRACTIONf_angle_d1.5676608
X-RAY DIFFRACTIONf_dihedral_angle_d18.4891808
X-RAY DIFFRACTIONf_chiral_restr0.059768
X-RAY DIFFRACTIONf_plane_restr0.008850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1881-3.38760.4251250.32942479X-RAY DIFFRACTION96
3.3876-3.64860.35461570.28372532X-RAY DIFFRACTION100
3.6486-4.01480.30751310.24842583X-RAY DIFFRACTION100
4.0148-4.59340.29021490.21432494X-RAY DIFFRACTION99
4.5934-5.77860.24291330.22562516X-RAY DIFFRACTION97
5.7786-27.73930.2681100.23122200X-RAY DIFFRACTION84

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