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- PDB-6drb: Crystal Structure of the YopH PTP1B WPD loop Chimera 3 PTPase bou... -

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Basic information

Entry
Database: PDB / ID: 6drb
TitleCrystal Structure of the YopH PTP1B WPD loop Chimera 3 PTPase bound to tungstate
ComponentsTargeted effector protein
KeywordsHYDROLASE / PTPase / phosphatase / PTP / YopH
Function / homology
Function and homology information


symbiont-mediated suppression of host reactive oxygen species generation / symbiont-mediated disruption of host focal adhesion / 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 superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...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 superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.745 Å
AuthorsMorales, Y. / Johnson, S.J. / Hengge, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112781 United States
National Science Foundation (NSF, United States)DBI1228874 United States
CitationJournal: Biochemistry / Year: 2018
Title: A YopH PTP1B Chimera Shows the Importance of the WPD-Loop Sequence to the Activity, Structure, and Dynamics of Protein Tyrosine Phosphatases.
Authors: Moise, G. / Morales, Y. / Beaumont, V. / Caradonna, T. / Loria, J.P. / Johnson, S.J. / Hengge, A.C.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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: Targeted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8362
Polymers33,5881
Non-polymers2481
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.743, 54.920, 97.848
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 Targeted effector protein / Type III secretion injected virulence protein / YopH


Mass: 33587.984 Da / Num. of mol.: 1 / Mutation: C235R, G352T, N353T, Q357F, T358G, A359V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yopH, YPCD1.67c / Plasmid: pD-Nus1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O68720
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4

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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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.1M Hepes pH7.5, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2016
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.745→50 Å / Num. obs: 7417 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 68.95 Å2 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.053 / Rrim(I) all: 0.164 / Χ2: 1.627 / Net I/av σ(I): 23 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.859.31.4991.56980.6020.5151.5870.918100
2.85-2.969.71.1067360.7610.3721.1680.959100
2.96-3.19.80.7987200.8740.2660.8421.039100
3.1-3.269.80.5817230.9220.1940.6131.152100
3.26-3.469.70.3837260.9590.1280.4041.356100
3.46-3.739.70.2337380.9810.0780.2461.65100
3.73-4.119.60.1557480.9920.0520.1641.87599.9
4.11-4.79.40.1087460.9950.0370.1142.342100
4.7-5.929.40.0947550.9960.0320.0992.101100
5.92-508.40.0718270.9940.0260.0752.8799.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4YAA

4yaa


Resolution: 2.745→36.868 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06
RfactorNum. reflection% reflection
Rfree0.2635 370 5.01 %
Rwork0.2128 --
obs0.2153 7383 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.44 Å2 / Biso mean: 74.9752 Å2 / Biso min: 43.5 Å2
Refinement stepCycle: final / Resolution: 2.745→36.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 5 0 2144
Biso mean--107.38 --
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022172
X-RAY DIFFRACTIONf_angle_d0.4742936
X-RAY DIFFRACTIONf_chiral_restr0.04339
X-RAY DIFFRACTIONf_plane_restr0.003387
X-RAY DIFFRACTIONf_dihedral_angle_d18.2021353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7455-3.14260.33021190.28372261238099
3.1426-3.95860.32731220.242323192441100
3.9586-36.87170.22071290.184424332562100
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)
11.46950.09981.64573.4737-0.47884.3751-0.13620.18370.05690.31260.4295-0.4666-0.58960.9853-0.36710.577-0.0117-0.02270.6585-0.17790.642-11.99917.767-20.709
21.72611.37240.60264.36780.35392.15410.0028-0.1869-0.160.28950.3194-0.54150.1480.2649-0.31780.67160.2281-0.08790.6401-0.07510.5731-14.943-0.552-13.956
30.7987-0.0560.7364.8971-1.94223.5731-0.13880.11130.0736-0.20170.50260.22990.11190.2073-0.28890.5363-0.00890.00810.5914-0.0890.5396-19.52210.822-27.962
42.00019.355-6.64752-0.482320.04860.0762-3.7869-0.2775-0.0786-0.0694-3.713-0.51780.01121.095-0.11010.00341.4438-0.32071.3952-5.8398.558-24.14
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 187:276 )A187 - 276
2X-RAY DIFFRACTION2( CHAIN A AND RESID 277:385 )A277 - 385
3X-RAY DIFFRACTION3( CHAIN A AND RESID 386:468 )A386 - 468
4X-RAY DIFFRACTION4( CHAIN A AND RESID 501:501 )A501

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