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- PDB-6dr7: YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate -

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Basic information

Entry
Database: PDB / ID: 6dr7
TitleYopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate
ComponentsTargeted effector protein
KeywordsHYDROLASE / PTPase / phosphatase / PTP / YopH
Function / homology
Function and homology information


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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / VANADATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsMoise, G. / Morales, 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

Downloads & links

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Assembly

Deposited unit
A: Targeted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8023
Polymers33,6281
Non-polymers1742
Water2,900161
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)49.697, 54.731, 96.537
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: 33628.004 Da / Num. of mol.: 1
Mutation: C235R, G352T, N353T, Q357F, T358G, A359V, V360P, S361E
Source method: isolated from a genetically manipulated source
Details: residues 163 to 186 not observed. / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-VO4 / VANADATE ION


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.95 Å3/Da / Density % sol: 37.05 % / Mosaicity: 1 °
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: 1.849→50 Å / Num. obs: 23225 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 27.72 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.054 / Rrim(I) all: 0.167 / Χ2: 1.148 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.929.11.6151.622560.6070.5611.7121.109100
1.92-1.999.31.09522900.7470.3761.161.187100
1.99-2.089.30.7622630.8570.2620.8051.32899.9
2.08-2.199.40.5223050.9210.1770.551.226100
2.19-2.339.30.38422810.9530.1320.4061.282100
2.33-2.519.40.27923110.9690.0950.2951.133100
2.51-2.769.40.2123320.9820.0710.2221.137100
2.76-3.169.40.1523260.9910.0510.1591.0599.9
3.16-3.999.10.10723570.9940.0370.1141.052100
3.99-508.80.08625040.9960.030.0920.98499.8

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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: 1.849→44.186 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.2084 1160 5.01 %
Rwork0.1735 --
obs0.1753 23173 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.73 Å2 / Biso mean: 32.5097 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 1.849→44.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 12 161 2345
Biso mean--53.01 38.97 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062225
X-RAY DIFFRACTIONf_angle_d0.7933015
X-RAY DIFFRACTIONf_chiral_restr0.051345
X-RAY DIFFRACTIONf_plane_restr0.004401
X-RAY DIFFRACTIONf_dihedral_angle_d18.6771390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8487-1.93280.32071410.300826832824
1.9328-2.03470.27541430.221726932836
2.0347-2.16220.25771430.203427202863
2.1622-2.32910.24891430.184327102853
2.3291-2.56350.22461430.175627472890
2.5635-2.93440.20191460.175327652911
2.9344-3.69670.17661460.161227772923
3.6967-44.19830.18531550.150929183073
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)
14.1684-0.0103-0.65415.58330.58995.16780.1951-0.3118-0.09590.3967-0.28960.4069-0.1649-0.69770.0540.25140.01690.0570.2993-0.02320.203113.288417.225140.1399
22.6521-0.18540.76171.4855-0.14193.1571-0.2837-0.12270.2458-0.0830.22190.1072-0.8454-0.49260.04750.3490.0755-0.01850.22350.02910.213911.34618.648416.1322
31.8129-0.6280.60471.9209-0.00942.14570.0206-0.0206-0.1134-0.17690.03660.27180.105-0.384-0.01950.2008-0.0581-0.02380.22880.01370.2119.07774.167710.4018
40.6844-0.54570.63213.15-2.31664.97270.10480.0501-0.1607-0.35640.15310.23330.6335-0.2326-0.26850.3227-0.1075-0.02030.2446-0.00380.273713.8809-4.31779.2868
52.31550.32630.20182.0097-1.52815.6815-0.0769-0.3367-0.08250.04370.00010.05490.292-0.22170.01920.1848-0.0441-0.01750.1594-0.01910.207314.298-0.415115.1915
65.72060.6875-3.98782.30180.5167.9660.077-0.4534-0.07480.2551-0.0092-0.0537-0.040.2599-0.14860.2256-0.0181-0.03860.1393-0.00960.209523.5549-1.777421.2402
77.0019-2.4835-4.11891.35380.4464.58790.2955-0.19881.4116-0.28950.2429-0.8543-0.52190.9776-0.51020.3081-0.09610.090.3846-0.04140.428330.39969.391910.2045
80.32010.1880.32012.60441.41924.18390.0283-0.0774-0.05210.22380.0169-0.10840.1359-0.1731-0.04130.19220.0040.00820.19880.02690.226817.553210.133230.4923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 208 )A187 - 208
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 263 )A209 - 263
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 305 )A264 - 305
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 338 )A306 - 338
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 358 )A339 - 358
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 385 )A359 - 385
7X-RAY DIFFRACTION7chain 'A' and (resid 386 through 398 )A386 - 398
8X-RAY DIFFRACTION8chain 'A' and (resid 399 through 468 )A399 - 468

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