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

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Basic information

Entry
Database: PDB / ID: 5jnt
TitleCrystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with MES
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: 1.45 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)18,6355
Polymers18,2381
Non-polymers3984
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint9 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.905, 55.018, 96.423
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: 18237.688 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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.47 Å3/Da / Density % sol: 50.11 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 20% PEG 3350, 200 mM NaCl, 40 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2015
RadiationMonochromator: mirrows / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.36→33.9 Å / Num. obs: 38952 / % possible obs: 97.8 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 25
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.36-1.381.60.227172.7
7.44-33.95.50.023187.2

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JNR

5jnr


Resolution: 1.45→33.9 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.444 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0503 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 1610 4.9 %RANDOM
Rwork0.1346 ---
obs0.1362 31159 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.69 Å2 / Biso mean: 15.964 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.45→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 24 275 1531
Biso mean--20.08 29.38 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0191343
X-RAY DIFFRACTIONr_bond_other_d0.0050.021270
X-RAY DIFFRACTIONr_angle_refined_deg3.0231.9711816
X-RAY DIFFRACTIONr_angle_other_deg1.27532935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38624.09166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76415242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1661511
X-RAY DIFFRACTIONr_chiral_restr0.3870.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021544
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_mcbond_it1.491.026650
X-RAY DIFFRACTIONr_mcbond_other1.4781.024649
X-RAY DIFFRACTIONr_mcangle_it2.3061.533823
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 122 -
Rwork0.153 2272 -
all-2394 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -3.137 Å / Origin y: 4.971 Å / Origin z: -11.096 Å
111213212223313233
T0.0079 Å2-0.0058 Å20 Å2-0.0084 Å2-0.0045 Å2--0.0061 Å2
L0.6437 °2-0.2075 °2-0.0574 °2-0.2386 °20.0832 °2--0.3957 °2
S0.0023 Å °0.0269 Å °-0.0341 Å °-0.016 Å °0.0176 Å °0.0038 Å °0.0379 Å °-0.0068 Å °-0.0199 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 157
2X-RAY DIFFRACTION1A201 - 204

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