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- PDB-5jnr: Crystal structure of human low molecular weight protein tyrosine ... -

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Basic information

Entry
Database: PDB / ID: 5jnr
TitleCrystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / protein tyrosine phosphatase / LMW-PTP / LMPTP
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm
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
Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)18,2101
Polymers18,2101
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.404, 55.863, 96.457
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 / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red ...LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase 1


Mass: 18209.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24666, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.4 Å3/Da / Density % sol: 48.69 % / Mosaicity: 0.48 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5 / Details: 7% PEG 10K, Bis Tris, Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2014
RadiationMonochromator: mirrows / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→36.51 Å / Num. obs: 12105 / % possible obs: 96.9 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Net I/σ(I): 34
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.238 / % possible all: 91.1

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8I

3n8i


Resolution: 2→36.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.807 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 574 4.9 %RANDOM
Rwork0.1634 ---
obs0.1658 11226 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.95 Å2 / Biso mean: 25.942 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 2→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 157 1386
Biso mean---36.1 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191333
X-RAY DIFFRACTIONr_bond_other_d0.0020.021244
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9511808
X-RAY DIFFRACTIONr_angle_other_deg1.04432876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6882465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2551511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02319
X-RAY DIFFRACTIONr_mcbond_it2.082.326663
X-RAY DIFFRACTIONr_mcbond_other2.062.324662
X-RAY DIFFRACTIONr_mcangle_it3.0243.477841
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 45 -
Rwork0.203 690 -
all-735 -
obs--81.4 %

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