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- PDB-5jnu: Crystal structure of mouse Low-Molecular Weight Protein Tyrosine ... -

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Basic information

Entry
Database: PDB / ID: 5jnu
TitleCrystal structure of mouse Low-Molecular Weight Protein Tyrosine Phosphatase type A (LMPTP-A) complexed with phosphate
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / protein tyrosine phosphatase / LMW-PTP / LMPTP
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / : / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.535 Å
AuthorsStanford, S.M. / Aleshin, A.E. / Liddington, R.C. / Bankston, L. / Cadwell, G. / Bottini, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK106233 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.
Authors: Stanford, S.M. / Aleshin, A.E. / Zhang, V. / Ardecky, R.J. / Hedrick, M.P. / Zou, J. / Ganji, S.R. / Bliss, M.R. / Yamamoto, F. / Bobkov, A.A. / Kiselar, J. / Liu, Y. / Cadwell, G.W. / ...Authors: Stanford, S.M. / Aleshin, A.E. / Zhang, V. / Ardecky, R.J. / Hedrick, M.P. / Zou, J. / Ganji, S.R. / Bliss, M.R. / Yamamoto, F. / Bobkov, A.A. / Kiselar, J. / Liu, Y. / Cadwell, G.W. / Khare, S. / Yu, J. / Barquilla, A. / Chung, T.D.Y. / Mustelin, T. / Schenk, S. / Bankston, L.A. / Liddington, R.C. / Pinkerton, A.B. / Bottini, N.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low molecular weight phosphotyrosine protein phosphatase
B: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8153
Polymers36,7202
Non-polymers951
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.384, 77.152, 92.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase / LMW-PTPase / Low molecular weight cytosolic acid phosphatase


Mass: 18359.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acp1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9D358, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.81 Å3/Da / Density % sol: 32.19 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 7% PEG 10K, Bis Tris, Ammonium Acetate; soaked in NaPO4 buffer before data collection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2015
RadiationMonochromator: mirrows / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.53→38.58 Å / Num. obs: 9354 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.074 / Rrim(I) all: 0.157 / Net I/σ(I): 6.7 / Num. measured all: 40453 / Scaling rejects: 76
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.53-2.653.30.6196.4
8.78-38.583.80.053198.8

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JNR

5jnr


Resolution: 2.535→38.576 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2534 477 5.12 %
Rwork0.2079 --
obs0.2103 9316 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.6 Å2 / Biso mean: 43.9639 Å2 / Biso min: 21.97 Å2
Refinement stepCycle: final / Resolution: 2.535→38.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 4 30 2494
Biso mean--56.24 39.11 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032531
X-RAY DIFFRACTIONf_angle_d0.5623411
X-RAY DIFFRACTIONf_chiral_restr0.041366
X-RAY DIFFRACTIONf_plane_restr0.003448
X-RAY DIFFRACTIONf_dihedral_angle_d14.2961558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5348-2.90150.30031460.25962869301598
2.9015-3.65520.26531630.217729043067100
3.6552-38.58040.23361680.186930663234100

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