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- PDB-6y2w: Crystal structure of the single mutant I16K of Low Molecular Weig... -

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Basic information

Entry
Database: PDB / ID: 6y2w
TitleCrystal structure of the single mutant 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
ACETATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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)17,9452
Polymers17,8861
Non-polymers591
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-1 kcal/mol
Surface area7920 Å2
Unit cell
Length a, b, c (Å)57.152, 41.760, 62.150
Angle α, β, γ (deg.)90.000, 96.573, 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-201-

ACT

21A-201-

ACT

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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: 17886.225 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris, 25% PEG3350, pH 6.5
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 PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→33.64 Å / Num. obs: 13623 / % possible obs: 94.05 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.03 / Net I/σ(I): 18.72
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1383 / CC1/2: 0.765 / Rpim(I) all: 0.33 / % possible all: 99.5

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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: 1.77→33.64 Å / SU ML: 0.2334 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1508
RfactorNum. reflection% reflection
Rfree0.1965 679 5.02 %
Rwork0.1634 --
obs0.165 13525 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.93 Å2
Refinement stepCycle: LAST / Resolution: 1.77→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 4 140 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291308
X-RAY DIFFRACTIONf_angle_d1.17891774
X-RAY DIFFRACTIONf_chiral_restr0.0603191
X-RAY DIFFRACTIONf_plane_restr0.008238
X-RAY DIFFRACTIONf_dihedral_angle_d6.3789180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.910.27251580.25172469X-RAY DIFFRACTION92.53
1.91-2.10.2021120.18332330X-RAY DIFFRACTION85.18
2.1-2.40.19231390.16322684X-RAY DIFFRACTION99.26
2.4-3.020.18141400.16562704X-RAY DIFFRACTION98.92
3.02-33.640.19471300.15032659X-RAY DIFFRACTION94.48
Refinement TLS params.Method: refined / Origin x: -17.8958308108 Å / Origin y: -0.924593738142 Å / Origin z: 17.2706834098 Å
111213212223313233
T0.224095404442 Å2-0.0249982524444 Å20.00961879993901 Å2-0.193773917305 Å2-0.00510240312629 Å2--0.192868452961 Å2
L1.74824755664 °20.355611616467 °20.389167402828 °2-1.39070461411 °2-0.335072282728 °2--1.06450978253 °2
S-0.166553758171 Å °0.0200420075129 Å °0.0255203655615 Å °-0.192867479841 Å °0.101702177767 Å °-0.0617306508037 Å °0.0339877279958 Å °-0.0649710095537 Å °-0.00116444835609 Å °
Refinement TLS groupSelection details: all

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