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- PDB-4z9a: Crystal structure of Low Molecular Weight Protein Tyrosine Phosph... -

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Basic information

Entry
Database: PDB / ID: 4z9a
TitleCrystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with phenylmethanesulfonic acid
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / protein-ligand complex / phenylmethanesulfonic acid
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
phenylmethanesulfonic acid / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTrivella, D.B.B. / Fonseca, E.M.B. / Scorsato, V. / Dias, M.P. / Aparicio, R.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/51602-5 Brazil
Sao Paulo Research Foundation (FAPESP)2010/17544-5 Brazil
Sao Paulo Research Foundation (FAPESP)2011/15792-4 Brazil
Sao Paulo Research Foundation (FAPESP)2011/03054-9 Brazil
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Crystal structures of the apo form and a complex of human LMW-PTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates.
Authors: Fonseca, E.M. / Trivella, D.B. / Scorsato, V. / Dias, M.P. / Bazzo, N.L. / Mandapati, K.R. / de Oliveira, F.L. / Ferreira-Halder, C.V. / Pilli, R.A. / Miranda, P.C. / Aparicio, R.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: 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

Downloads & links

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Assembly

Deposited unit
A: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2125
Polymers18,7551
Non-polymers4564
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.750, 55.230, 97.800
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: 18755.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% (w/v) PEG 5000, 0.2 M ammonium sulfate, 0.2 M MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.1→32.6 Å / Num. obs: 10699 / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAVersion 3.3.16data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 2.1→28.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.831 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23511 796 7.5 %RANDOM
Rwork0.17909 ---
obs0.1832 9846 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.1→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 27 88 1345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191294
X-RAY DIFFRACTIONr_bond_other_d0.0010.021208
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9741748
X-RAY DIFFRACTIONr_angle_other_deg0.87332782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88823.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88115229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3171512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3043.11619
X-RAY DIFFRACTIONr_mcbond_other2.2583.103618
X-RAY DIFFRACTIONr_mcangle_it3.2884.642773
X-RAY DIFFRACTIONr_mcangle_other3.2944.65774
X-RAY DIFFRACTIONr_scbond_it2.8133.505675
X-RAY DIFFRACTIONr_scbond_other2.8123.507676
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2045.151974
X-RAY DIFFRACTIONr_long_range_B_refined6.41325.7681516
X-RAY DIFFRACTIONr_long_range_B_other6.41125.7831517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 69 -
Rwork0.267 682 -
obs--97.15 %
Refinement TLS params.Method: refined / Origin x: 3.0116 Å / Origin y: 4.9277 Å / Origin z: 11.3402 Å
111213212223313233
T0.0982 Å20.046 Å2-0.0408 Å2-0.0775 Å2-0.0409 Å2--0.0378 Å2
L0.8448 °20.4947 °2-0.0151 °2-0.2997 °2-0.0172 °2--1.6205 °2
S0.1052 Å °0.0565 Å °0.0006 Å °0.0632 Å °0.0619 Å °-0.0127 Å °0.3014 Å °0.0488 Å °-0.1671 Å °

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