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- PDB-6dr9: Crystal Structure of the YopH PTP1B Chimera 3 PTPase apo form -

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Basic information

Entry
Database: PDB / ID: 6dr9
TitleCrystal Structure of the YopH PTP1B Chimera 3 PTPase apo form
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
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 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


Theoretical massNumber of molelcules
Total (without water)33,5881
Polymers33,5881
Non-polymers00
Water4,071226
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)49.808, 53.772, 103.196
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.06 Å3/Da / Density % sol: 40.21 % / Mosaicity: 0.652 °
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: Apr 15, 2016 / 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: 1.945→50 Å / Num. obs: 20100 / % possible obs: 95.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.05 / Rrim(I) all: 0.184 / Χ2: 1.039 / Net I/av σ(I): 14.4 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0212.51.7321.418950.6060.4871.8010.93992.1
2.02-2.112.51.25219100.730.3521.3031.0292.9
2.1-2.212.50.9119160.820.2560.9471.08193.2
2.2-2.3112.50.67519140.9350.1910.7031.10892.4
2.31-2.4612.30.51819550.9350.1470.5391.11293.4
2.46-2.6512.10.37419950.9660.1070.391.1195.7
2.65-2.9112.20.25320260.9820.0730.2641.08597.4
2.91-3.3312.50.14721210.9950.0430.1541.07499.4
3.33-4.213.30.07821170.9980.0220.0811.00199.7
4.2-5013.40.0522510.9990.0140.0520.90199.2

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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: 1.945→29.82 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.52
RfactorNum. reflection% reflection
Rfree0.2173 1003 5 %
Rwork0.1758 --
obs0.1779 20059 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.51 Å2 / Biso mean: 28.7265 Å2 / Biso min: 11.7 Å2
Refinement stepCycle: final / Resolution: 1.945→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 0 226 2366
Biso mean---37.79 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032166
X-RAY DIFFRACTIONf_angle_d0.6162926
X-RAY DIFFRACTIONf_chiral_restr0.043338
X-RAY DIFFRACTIONf_plane_restr0.004386
X-RAY DIFFRACTIONf_dihedral_angle_d19.0441350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9454-2.0480.3111330.27312542267591
2.048-2.17630.26191390.21162604274393
2.1763-2.34420.26111370.19572611274893
2.3442-2.580.22741360.1842659279594
2.58-2.95310.25971470.1692781292898
2.9531-3.71940.19421530.164228513004100
3.7194-29.82370.17851580.157330083166100
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)
10.94550.0882-0.65011.22950.39351.74180.020.12190.02430.159-0.03340.33170.1671-0.3696-0.04450.2566-0.04660.00820.1516-0.00880.2348-15.4642.6863-28.6067
21.65650.0928-0.03040.66290.36092.0175-0.0545-0.09640.01220.12450.00310.06350.2226-0.146-0.00040.1574-0.00690.01080.17040.03340.1595-12.305915.2087-12.2197
30.7584-0.1421-0.41810.72010.05390.35920.119-0.01710.145-0.14290.0340.15290.0148-0.10290.00030.15490.02120.00140.16520.0320.1949-8.862726.9841-14.7201
40.43990.37850.1481.76470.94751.36490.0010.0635-0.0576-0.19320.0186-0.0272-0.0660.0045-00.16310.01660.01230.14310.02440.158-4.468216.2283-26.996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 188 through 227 )A188 - 227
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 317 )A228 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 361 )A318 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 468 )A362 - 468

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