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- PDB-6dt6: Crystal Structure of the YopH PTP1B Chimera 3 PTPase bound to vanadate -

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Basic information

Entry
Database: PDB / ID: 6dt6
TitleCrystal Structure of the YopH PTP1B Chimera 3 PTPase bound to vanadate
ComponentsTargeted effector protein
KeywordsHYDROLASE / PTPase / phosphatase / PTP / YopH
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 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, 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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 15, 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)33,7032
Polymers33,5881
Non-polymers1151
Water1,892105
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)49.125, 54.781, 96.791
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
Source method: isolated from a genetically manipulated source
Details: Residues 163-186 not visible / 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-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.56 % / Mosaicity: 0.732 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: Hepes, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2014 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15742 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.077 / Rrim(I) all: 0.171 / Χ2: 2.107 / Net I/av σ(I): 15.9 / 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
2.1-2.184.40.9561.615290.5690.4941.0821.04299.8
2.18-2.264.70.7915390.830.3960.8881.13599.7
2.26-2.374.90.61815540.7650.3030.6911.24499.9
2.37-2.494.90.49115520.8250.2420.551.36599.7
2.49-2.654.90.37315530.8880.1840.4181.52699.9
2.65-2.854.80.29115690.9290.1430.3261.93499.7
2.85-3.144.80.21715600.9610.1070.2432.4299.8
3.14-3.594.50.14715810.980.0740.1663.20599.4
3.59-4.524.40.09916080.990.0510.1123.86599.3
4.52-504.40.07616970.9920.040.0873.4699.1

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Processing

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

4yaa


Resolution: 2.101→36.573 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.26
RfactorNum. reflection% reflection
Rfree0.2268 786 5.01 %
Rwork0.1745 --
obs0.177 15697 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 42.4382 Å2 / Biso min: 21.78 Å2
Refinement stepCycle: final / Resolution: 2.101→36.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 5 105 2279
Biso mean--60.79 47.34 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082205
X-RAY DIFFRACTIONf_angle_d0.8762983
X-RAY DIFFRACTIONf_chiral_restr0.053342
X-RAY DIFFRACTIONf_plane_restr0.005395
X-RAY DIFFRACTIONf_dihedral_angle_d8.7831897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1007-2.23230.30041250.23492391251698
2.2323-2.40460.25231300.206224372567100
2.4046-2.64660.24621300.189524772607100
2.6466-3.02940.25861290.184724842613100
3.0294-3.8160.2111330.170824952628100
3.816-36.57880.20461390.15442627276699
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)
10.82380.20350.90141.36620.57243.1915-0.1413-0.05890.0537-0.19620.12650.1009-0.4285-0.3843-0.01020.27550.01610.00760.28120.04170.301612.421815.677819.7531
22.0964-0.51110.96812.8785-0.25511.18780.019-0.0498-0.2549-0.03060.06950.28590.3238-0.2396-0.1160.3314-0.0928-0.040.32720.0130.354310.548-1.793111.5867
33.30610.3656-2.8191.87030.12625.0653-0.022-0.27880.09870.31140.0889-0.16560.02270.3048-0.02880.3451-0.0156-0.02680.3045-0.00920.299723.2123-1.751421.3604
40.36370.11260.19332.01080.82262.9637-0.0324-0.09630.02330.18050.0885-0.0916-0.0209-0.1138-0.06330.2542-0.0012-0.00240.29150.0250.297919.26299.930627.5913
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 357 )A288 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 385 )A358 - 385
4X-RAY DIFFRACTION4chain 'A' and (resid 386 through 468 )A386 - 468

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