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- PDB-7mpd: Structure of SsoPTP bound to 2-chloroethylsulfonate -

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Basic information

Entry
Database: PDB / ID: 7mpd
TitleStructure of SsoPTP bound to 2-chloroethylsulfonate
ComponentsSsoPTP
KeywordsHYDROLASE / protein tyrosine phosphatase / 2-chloroethylsuflonate / SsoPTP
Function / homology
Function and homology information


dephosphorylation / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain ...Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
2-chloroethane-1-sulfonic acid / Protein phosphatase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsPinkston, J.A. / Olsen, K.J. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112781 United States
CitationJournal: Biochemistry / Year: 2021
Title: Significant Loop Motions in the SsoPTP Protein Tyrosine Phosphatase Allow for Dual General Acid Functionality.
Authors: Pinkston, J. / Jo, J. / Olsen, K.J. / Comer, D. / Glaittli, C.A. / Loria, J.P. / Johnson, S.J. / Hengge, A.C.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: SsoPTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8163
Polymers18,4331
Non-polymers3832
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.923, 83.923, 42.352
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein SsoPTP


Mass: 18433.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VZ7
#2: Chemical ChemComp-ZLJ / 2-chloroethane-1-sulfonic acid


Mass: 144.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5ClO3S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 0.001 M zinc chloride, 20% PEG 6000

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Data collection

DiffractionMean temperature: 84 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 78794 / % possible obs: 99.1 % / Redundancy: 17 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.019 / Rrim(I) all: 0.081 / Χ2: 1.039 / Net I/σ(I): 18.1 / Num. measured all: 1339872
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.05-1.099.40.66372310.8940.2190.71.191.4
1.09-1.1315.30.41378840.9760.1070.4271.06599.8
1.13-1.1817.10.29779200.9850.0730.3061.077100
1.18-1.2416.70.22679110.990.0560.2331.06899.9
1.24-1.3217.90.17679350.9920.0420.1811.034100
1.32-1.4317.20.13979410.9950.0340.1441.01199.9
1.43-1.5718.70.1179320.9970.0260.1131.01299.9
1.57-1.818.30.09179240.9970.0220.0941.02199.9
1.8-2.2619.50.07879920.9980.0180.081.01899.8
2.26-5019.10.07181240.9970.0170.0731.03299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.89 Å36.59 Å
Translation4.89 Å36.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I6I

2i6i


Resolution: 1.05→36.59 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1377 1996 2.53 %
Rwork0.1252 --
obs0.1255 78770 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.05→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 43 185 1519
Biso mean--60.36 33.42 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131445
X-RAY DIFFRACTIONf_angle_d1.2341974
X-RAY DIFFRACTIONf_dihedral_angle_d19.751213
X-RAY DIFFRACTIONf_chiral_restr0.088210
X-RAY DIFFRACTIONf_plane_restr0.008250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.080.19291260.1738485688
1.08-1.10.15011450.1344541098
1.1-1.140.11561390.115514100
1.14-1.170.11911460.09625496100
1.17-1.220.10821440.09465500100
1.22-1.260.11471400.09135520100
1.26-1.320.12121490.09475552100
1.32-1.390.11011440.09315487100
1.39-1.480.10921470.09415540100
1.48-1.590.10421400.09265556100
1.59-1.750.12541460.10485541100
1.75-2.010.14031380.12235554100
2.01-2.530.14671480.13285561100
2.53-36.590.15491440.14995687100

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