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- PDB-6y2v: Crystal structure of the double mutant L13R I16K of Low Molecular... -

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Basic information

Entry
Database: PDB / ID: 6y2v
TitleCrystal structure of the double mutant L13R I16K of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP)
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / Engineered
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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLevy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom) United Kingdom
CitationJournal: Plos One / Year: 2020
Title: Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme.
Authors: Egbe, E. / Levy, C.W. / Tabernero, L.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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)18,3073
Polymers18,0611
Non-polymers2452
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-5 kcal/mol
Surface area8040 Å2
Unit cell
Length a, b, c (Å)56.625, 41.287, 56.898
Angle α, β, γ (deg.)90.000, 91.809, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

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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: 18061.457 Da / Num. of mol.: 1 / Mutation: L13R I16K
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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris, 25% PEG3350, pH 5.5 / Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→33.36 Å / Num. obs: 9025 / % possible obs: 99.04 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Net I/σ(I): 9.87
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 917 / CC1/2: 0.718 / Rpim(I) all: 0.38 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWW

1xww


Resolution: 2→33.36 Å / SU ML: 0.1666 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8789
RfactorNum. reflection% reflection
Rfree0.2313 480 5.33 %
Rwork0.1826 --
obs0.1851 8999 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.64 Å2
Refinement stepCycle: LAST / Resolution: 2→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 15 91 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021274
X-RAY DIFFRACTIONf_angle_d0.47221717
X-RAY DIFFRACTIONf_chiral_restr0.0417185
X-RAY DIFFRACTIONf_plane_restr0.0025224
X-RAY DIFFRACTIONf_dihedral_angle_d22176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.280.271520.21812845X-RAY DIFFRACTION99.67
2.28-2.880.23051670.20342800X-RAY DIFFRACTION98.74
2.88-33.360.22061610.16362874X-RAY DIFFRACTION98.73
Refinement TLS params.Method: refined / Origin x: -14.7011401931 Å / Origin y: 0.816287854349 Å / Origin z: 14.4902950662 Å
111213212223313233
T0.143698803236 Å2-0.0216325822911 Å2-0.00639128211815 Å2-0.0926114316889 Å2-0.011848539913 Å2--0.149009215908 Å2
L2.40797055093 °20.110582959028 °20.0371187442019 °2-1.52087509212 °2-0.520301477122 °2--2.46340331247 °2
S-0.036966907399 Å °0.00779418956184 Å °0.122328057007 Å °-0.154587303733 Å °0.0494780387223 Å °-0.00841851569211 Å °0.0148800272328 Å °-0.163075767341 Å °-0.00266504562326 Å °
Refinement TLS groupSelection details: all

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