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- PDB-4z9b: Crystal structure of Low Molecular Weight Protein Tyrosine Phosph... -

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Basic information

Entry
Database: PDB / ID: 4z9b
TitleCrystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / protein-ligand complex / benzylphosphonic acid
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome ...acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning 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
benzylphosphonic acid / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsFonseca, E.M.B. / Trivella, D.B.B. / Scorsato, V. / Dias, M.P. / de Oliveira, F.L. / Miranda, P.C.M.L. / 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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)18,9272
Polymers18,7551
Non-polymers1721
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.088, 54.287, 97.468
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-B85 / benzylphosphonic acid


Mass: 172.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 32% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 9, 2013
RadiationMonochromator: Quazar(TM) Cu multilayer optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→27.8 Å / Num. obs: 7097 / % possible obs: 99.7 % / Redundancy: 11.84 % / Rmerge(I) obs: 0.1455 / Net I/σ(I): 16.34
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 11.58 % / Rmerge(I) obs: 0.5618 / Mean I/σ(I) obs: 2.94 / % possible all: 100

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Processing

Software
NameVersionClassification
APEXdata collection
APEXdata reduction
APEXdata scaling
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 2.41→27.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.877 / SU B: 22.849 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.539 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30148 325 4.7 %RANDOM
Rwork0.21479 ---
obs0.21875 6641 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.003 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å2-0 Å20 Å2
2---1.7 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.41→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 11 69 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191297
X-RAY DIFFRACTIONr_bond_other_d0.0010.021200
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9591753
X-RAY DIFFRACTIONr_angle_other_deg0.8932759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45623.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4621511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
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_it1.5022.373630
X-RAY DIFFRACTIONr_mcbond_other1.5022.368629
X-RAY DIFFRACTIONr_mcangle_it2.5133.54785
X-RAY DIFFRACTIONr_mcangle_other2.5123.546786
X-RAY DIFFRACTIONr_scbond_it1.3932.552667
X-RAY DIFFRACTIONr_scbond_other1.3932.553668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3343.767967
X-RAY DIFFRACTIONr_long_range_B_refined4.63518.9571498
X-RAY DIFFRACTIONr_long_range_B_other4.63418.9671499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.52 32 -
Rwork0.358 488 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94463.821-5.58054.9673-7.234610.58390.18220.19230.24930.24660.27870.3279-0.3238-0.3429-0.46090.07280.05790.03250.10750.01930.0672-9.1617-3.153138.7355
21.2640.4187-0.11380.26730.11561.1172-0.0566-0.103-0.0964-0.04040.1024-0.05580.05460.0543-0.04590.110.02730.02040.1839-0.00520.0153.31274.624711.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - -1
2X-RAY DIFFRACTION2A5 - 157

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