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- PDB-7uw6: The co-crystal structure of low molecular weight protein tyrosine... -

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Basic information

Entry
Database: PDB / ID: 7uw6
TitleThe co-crystal structure of low molecular weight protein tyrosine phosphatase (LMW-PTP) with a small molecule inhibitor SPAA-2
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / low molecular weight protein tyrosine phosphatase / 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 / cytoplasmic side of plasma membrane / sarcolemma / 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
Chem-OIF / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, J. / Zhang, Z.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA207288 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)RO1 069202 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Design of Active-Site-Directed, Highly Potent, Selective, and Orally Bioavailable Low-Molecular-Weight Protein Tyrosine Phosphatase Inhibitors.
Authors: He, R. / Wang, J. / Yu, Z.H. / Moyers, J.S. / Michael, M.D. / Durham, T.B. / Cramer, J.W. / Qian, Y. / Lin, A. / Wu, L. / Noinaj, N. / Barrett, D.G. / Zhang, Z.Y.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)20,3782
Polymers20,1061
Non-polymers2721
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.873, 54.566, 95.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase / LMW-PTP / LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase ...LMW-PTP / LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase 1


Mass: 20105.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: L35 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-OIF / 2-[(1,3-benzothiazol-2-yl)amino]-2-oxoethane-1-sulfonic acid


Mass: 272.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystallization buffer grid is 25-30% PEGME 5000 in 100 mM Bis-Tris, pH 6.0-6.5. The final concentration of the ligand in the crystallization solution is 1 mM.
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 29659 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.045 / Χ2: 0.692 / Net I/σ(I): 6.4 / Num. measured all: 123876
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.5340.000114670.474199.4
1.53-1.554.10.000114690.487199.9
1.55-1.584.10.85714730.496199.9
1.58-1.624.20.76114600.531199.8
1.62-1.654.10.62314640.5111100
1.65-1.694.10.49814870.517199.8
1.69-1.734.10.40114620.557199.9
1.73-1.784.10.3414560.566199.6
1.78-1.834.10.26815000.585199.8
1.83-1.894.20.19714640.662199.5
1.89-1.964.20.16214800.763199.3
1.96-2.044.20.12614910.8541100
2.04-2.134.20.10614560.923199.2
2.13-2.244.20.09114830.964199
2.24-2.384.20.07814840.928198.9
2.38-2.564.20.06414831.03198.6
2.56-2.824.30.04715031.007198.8
2.82-3.234.30.03114930.731197.4
3.23-4.074.30.02215160.595197.9
4.07-504.10.02215680.597194.4

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 1.5→21.82 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 2000 6.76 %
Rwork0.1611 27607 -
obs0.1633 29607 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.52 Å2 / Biso mean: 28.6135 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 1.5→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 25 219 1474
Biso mean--22.22 42.21 -
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.33391400.29221938207899
1.54-1.580.30021440.271319712115100
1.58-1.630.27071390.239119322071100
1.63-1.680.23581410.211519472088100
1.68-1.740.25111450.196819872132100
1.74-1.810.2251410.195119622103100
1.81-1.890.19891420.168219532095100
1.89-1.990.17191420.156819542096100
1.99-2.110.21491430.15861976211999
2.11-2.280.20531430.16211971211499
2.28-2.510.18041420.16131978212098
2.51-2.870.22941450.16731987213299
2.87-3.610.16131430.15231989213298
3.61-21.820.17131500.13422062221296
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)
12.44930.4853-0.03162.20240.65081.79940.0674-0.0282-0.02870.05810.0462-0.1624-0.11710.1224-0.1180.19110.0215-0.02770.1715-0.01350.184418.1651-3.120913.5174
22.21542.83530.53546.53542.84121.9350.2535-0.1439-0.15470.5504-0.0007-0.42930.05610.1857-0.23190.28260.009-0.08080.2277-0.0260.222820.7419-2.656420.8262
31.698-0.25540.15151.3007-0.06631.4110.06570.1776-0.18620.0066-0.0093-0.3085-0.0060.1008-0.04250.16540.0235-0.02160.1934-0.04790.209620.1686-9.62216.9979
41.48290.5405-0.07791.33-0.33592.06270.05050.0595-0.12430.0270.05530.12570.0444-0.3059-0.10120.18410.0258-0.03950.2461-0.00420.20044.6261-11.582313.917
51.69370.3845-0.0761.08390.34491.28020.03580.26590.2052-0.1633-0.07710.0963-0.3529-0.31980.01640.25170.0952-0.04070.24720.01850.25298.34160.1285.2049
62.1850.5288-0.38961.7661-0.13953.12630.0290.02110.40620.03710.068-0.0032-0.5248-0.0716-0.14380.28640.0501-0.01350.18970.00890.30314.0854.75938.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )A4 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 45 )A33 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 84 )A46 - 84
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 111 )A85 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 134 )A112 - 134
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 157 )A135 - 157

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