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- PDB-5kqm: Co-crystal structure of LMW-PTP in complex with MES -

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Basic information

Entry
Database: PDB / ID: 5kqm
TitleCo-crystal structure of LMW-PTP in complex with MES
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / LMW-PTP / Inhibitor / Complex
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: 1.91 Å
AuthorsWang, J. / Zhang, Z.-Y. / Yu, Z.-H.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Inhibition of low molecular weight protein tyrosine phosphatase by an induced-fit mechanism.
Authors: He, R. / Wang, J. / Yu, Z.H. / Zhang, R.Y. / Liu, S. / Wu, L. / Zhang, Z.Y.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)20,4322
Polymers20,2371
Non-polymers1951
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.690, 54.826, 95.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 20236.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES, pH=6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 14276 / % possible obs: 99.7 % / Redundancy: 6.6 % / Net I/σ(I): 27.7

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 1.91→27.463 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02
RfactorNum. reflection% reflection
Rfree0.2281 715 5.02 %
Rwork0.1847 --
obs0.1869 14231 99.22 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 35.385 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2987 Å20 Å2-0 Å2
2--5.4378 Å20 Å2
3----5.7365 Å2
Refinement stepCycle: LAST / Resolution: 1.91→27.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 12 121 1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081260
X-RAY DIFFRACTIONf_angle_d1.9891700
X-RAY DIFFRACTIONf_dihedral_angle_d16.006483
X-RAY DIFFRACTIONf_chiral_restr0.076182
X-RAY DIFFRACTIONf_plane_restr0.004222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.05520.2581490.22312567X-RAY DIFFRACTION97
2.0552-2.26190.26221440.20162687X-RAY DIFFRACTION100
2.2619-2.5890.2751420.19932697X-RAY DIFFRACTION100
2.589-3.2610.24211280.19362717X-RAY DIFFRACTION100
3.261-27.46550.19711520.16812848X-RAY DIFFRACTION99

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