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- PDB-5jnv: Crystal structure of bovine low molecular weight protein tyrosine... -

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Basic information

Entry
Database: PDB / ID: 5jnv
TitleCrystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with HEPES
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 / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5555
Polymers18,0821
Non-polymers4734
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint13 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.944, 122.939, 44.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 18082.432 Da / Num. of mol.: 1 / Mutation: W49Y N50E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ACP1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11064, protein-tyrosine-phosphatase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 20% PEG 3350, 0.2 M NaCl, Bis Tris, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 1.52→36.25 Å / Num. obs: 24753 / % possible obs: 96.1 % / Redundancy: 4.2 % / CC1/2: 0.943 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.52-1.552.50.388154.1
8.34-36.254.10.053198.3

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PNT

1pnt


Resolution: 1.6→36.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.413 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0825 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1108 5 %RANDOM
Rwork0.1536 ---
obs0.156 20881 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.89 Å2 / Biso mean: 21.163 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.6→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 27 221 1480
Biso mean--25.12 33.11 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.021378
X-RAY DIFFRACTIONr_bond_other_d0.0030.021294
X-RAY DIFFRACTIONr_angle_refined_deg2.9511.961872
X-RAY DIFFRACTIONr_angle_other_deg1.3382.9962976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31124.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1131513
X-RAY DIFFRACTIONr_chiral_restr0.1940.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021614
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02331
X-RAY DIFFRACTIONr_mcbond_it1.331.202667
X-RAY DIFFRACTIONr_mcbond_other1.3221.2666
X-RAY DIFFRACTIONr_mcangle_it2.0041.797846
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 67 -
Rwork0.189 1518 -
all-1585 -
obs--98.33 %
Refinement TLS params.Method: refined / Origin x: -16.353 Å / Origin y: -17.847 Å / Origin z: 0.077 Å
111213212223313233
T0.0475 Å20.0087 Å2-0.0142 Å2-0.009 Å2-0.0017 Å2--0.0141 Å2
L0.6458 °2-0.3592 °2-0.4192 °2-0.8251 °2-0.1819 °2--1.6544 °2
S-0.0343 Å °0.0206 Å °0.0376 Å °0.0489 Å °0.0321 Å °-0.0596 Å °-0.1644 Å °-0.0481 Å °0.0022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 157
2X-RAY DIFFRACTION1A201 - 203

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