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- PDB-7l0i: Ligand-free YopH G352T -

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Basic information

Entry
Database: PDB / ID: 7l0i
TitleLigand-free YopH G352T
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / Protein tyrosine phosphatase, catalytic domain / 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 ...Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / Protein tyrosine phosphatase, catalytic domain / 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
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsShen, R.D. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01GM112781 United States
CitationJournal: Jacs Au / Year: 2021
Title: Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.
Authors: Shen, R. / Crean, R.M. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8362
Polymers33,5981
Non-polymers2381
Water2,540141
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)49.135, 56.296, 98.335
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 Protein-tyrosine-phosphatase


Mass: 33597.938 Da / Num. of mol.: 1 / Mutation: G352T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria)
Gene: yopH, Y0013, YPCD1.67c, G4D65_20050, G4D67_19670, GD372_22270
Production host: Escherichia coli (E. coli) / References: UniProt: O68720, protein-tyrosine-phosphatase
#2: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, and 15-34 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 17704 / % possible obs: 95.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.079 / Rrim(I) all: 0.198 / Χ2: 1.051 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.130.9614310.4670.5781.1331.00279.6
2.1-2.193.70.66816340.7040.3640.7671.06789.3
2.19-2.294.10.63117380.7630.3270.7161.08294.5
2.29-2.414.60.53217150.8730.2610.5961.05195
2.41-2.5650.46617240.9160.2190.5181.07593.3
2.56-2.766.40.418360.950.1690.4361.07499.6
2.76-3.0370.29118520.9620.1180.3151.027100
3.03-3.476.70.18918670.9840.0770.2051.04799.8
3.47-4.377.10.1219040.9920.0470.1291.04699.8
4.37-506.50.08620030.9960.0350.0931.03999.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YAA

4yaa


Resolution: 2.02→49.17 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 875 4.99 %
Rwork0.2017 16674 -
obs0.2043 17549 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.37 Å2 / Biso mean: 34.9746 Å2 / Biso min: 22.07 Å2
Refinement stepCycle: final / Resolution: 2.02→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 15 141 2270
Biso mean--41.99 35.79 -
Num. residues----282
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.140.37521230.3489226479
2.14-2.310.32471380.2742269894
2.31-2.540.38041410.2365272394
2.54-2.910.25571550.21162940100
2.91-3.660.25721550.18552958100
3.66-49.170.17971630.15443091100
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)
10.6582-0.080.37131.2307-0.86371.86630.01310.00220.16310.1064-0.04860.0306-0.08660.07670.0260.17450.0090.03050.1811-0.02340.4606-12.567516.6721-20.2158
21.7390.5144-0.71570.5046-0.07611.175-0.0281-0.0987-0.13930.0179-0.0594-0.02550.10670.04070.08630.24730.0108-0.01490.20460.01180.5567-14.2312-0.4491-14.4977
31.0970.13860.74472.7594-0.41391.9742-0.06230.00150.1096-0.07410.01710.2236-0.0077-0.05030.03140.20930.01030.01840.2008-0.00840.4675-19.334711.338-28.3808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 287 )A187 - 287
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 386 )A288 - 386
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 468 )A387 - 468

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