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- PDB-5kql: Co-crystal structure of LMW-PTP in complex with 2-oxo-1-phenyl-2-... -

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Basic information

Entry
Database: PDB / ID: 5kql
TitleCo-crystal structure of LMW-PTP in complex with 2-oxo-1-phenyl-2-(phenylamino)ethanesulfonic acid
ComponentsLow molecular weight phosphotyrosine protein phosphatase
Keywordshydrolase/hydrolase inhibitor / LMW-PTP / Inhibitor / Complex / hydrolase-hydrolase 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 / SH3 domain binding / cytoplasmic side of plasma membrane / chemical synaptic transmission / synapse ...acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / SH3 domain binding / cytoplasmic side of plasma membrane / chemical synaptic transmission / synapse / extracellular exosome / cytoplasm / 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
Chem-6VY / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)20,5282
Polymers20,2371
Non-polymers2911
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.190, 54.573, 97.515
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-6VY / (1~{S})-2-oxidanylidene-1-phenyl-2-phenylazanyl-ethanesulfonic acid


Mass: 291.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25-30% PEGME 5000, 100 mM Bis-Tris, pH 6.0-6.5 / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 33262 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 24.4

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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: 1.45→21.629 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.75
RfactorNum. reflection% reflection
Rfree0.1765 1680 5.06 %
Rwork0.164 --
obs0.1647 33197 99.9 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Bsol: 44.303 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9368 Å2-0 Å20 Å2
2--2.1861 Å20 Å2
3----1.2493 Å2
Refinement stepCycle: LAST / Resolution: 1.45→21.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 20 268 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061307
X-RAY DIFFRACTIONf_angle_d1.0951774
X-RAY DIFFRACTIONf_dihedral_angle_d12.777502
X-RAY DIFFRACTIONf_chiral_restr0.076192
X-RAY DIFFRACTIONf_plane_restr0.006233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.49210.26281180.23132607X-RAY DIFFRACTION99
1.4921-1.54020.22521340.19882561X-RAY DIFFRACTION100
1.5402-1.59530.21791400.1742590X-RAY DIFFRACTION100
1.5953-1.65910.20441350.17032602X-RAY DIFFRACTION100
1.6591-1.73460.18311420.15362576X-RAY DIFFRACTION100
1.7346-1.8260.17621530.15712595X-RAY DIFFRACTION100
1.826-1.94030.19551360.16632614X-RAY DIFFRACTION100
1.9403-2.090.18611410.1642605X-RAY DIFFRACTION100
2.09-2.30020.20511320.16372658X-RAY DIFFRACTION100
2.3002-2.63250.18351330.1692650X-RAY DIFFRACTION100
2.6325-3.31470.18051500.16332654X-RAY DIFFRACTION100
3.3147-21.6310.13721660.15142805X-RAY DIFFRACTION100

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