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- PDB-7l0m: Vanadate-bound YopH G352T -

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Basic information

Entry
Database: PDB / ID: 7l0m
TitleVanadate-bound YopH G352T
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


symbiont-mediated disruption of host focal adhesion / symbiont-mediated suppression of host reactive oxygen species generation / 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, 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
VANADATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)33,7132
Polymers33,5981
Non-polymers1151
Water2,558142
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)49.231, 56.091, 98.302
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-VO4 / VANADATE ION


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 39.1 %
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→50 Å / Num. obs: 18343 / % possible obs: 96.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.064 / Rrim(I) all: 0.189 / Χ2: 1.037 / Net I/σ(I): 6.3 / Num. measured all: 140771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0750.64815360.7960.2780.711.03382.5
2.07-2.156.20.50816690.9280.1930.5471.08889.3
2.15-2.256.70.46817660.9240.1760.5031.06894.6
2.25-2.377.20.43518130.9470.1630.4661.01197.5
2.37-2.527.50.36118710.970.1370.3881.0499.3
2.52-2.718.80.30318840.9760.1040.3211.09299.9
2.71-2.998.80.22418980.9870.0780.2381.03199.9
2.99-3.428.40.1819180.9870.0640.1921.04199.9
3.42-4.3190.13719200.9920.0460.1451.02699.8
4.31-508.30.11120680.9930.040.1180.96799.9

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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→49.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 914 5 %
Rwork0.178 17355 -
obs0.1805 18269 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.19 Å2 / Biso mean: 32.4515 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 2→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 5 142 2259
Biso mean--28.15 35.72 -
Num. residues----282
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 (%)
2-2.10.30581080.25652046215481
2.1-2.240.22531250.21212354247992
2.24-2.410.29471310.20452490262197
2.41-2.650.25131330.186325302663100
2.65-3.030.22381350.186925782713100
3.03-3.820.20821380.165126212759100
3.82-49.150.20231440.154327362880100
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)
12.0410.19560.2842.68951.04565.3508-0.05420.3135-0.1591-0.2814-0.0669-0.20870.24970.36440.08760.27210.04580.06480.22550.02770.3932-13.499218.1524-41.1361
21.89790.2115-0.1873.3941-0.89941.42520.0548-0.12730.37170.2463-0.04020.0987-0.17050.0432-0.00870.1520.00110.0120.1695-0.05180.2697-12.338315.85-14.4954
31.34140.425-0.05550.29320.02461.18310.007-0.0448-0.0180.0109-0.0381-0.05440.09360.02520.02240.24340.0134-0.00330.1955-0.01910.3865-14.1819-0.8509-14.2298
43.35780.4277-0.6881.38221.63642.38580.2486-0.3150.77080.66290.0931.6533-0.8783-1.3867-0.36110.3720.14680.11570.57090.04030.7192-30.345210.1543-10.7979
50.79530.01310.68271.1179-0.07661.8977-0.03370.05350.1403-0.1714-0.05410.1046-0.0122-0.06590.07860.2240.01160.00780.1998-0.0270.3539-17.874411.0239-30.8333
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 287 )A209 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 385 )A288 - 385
4X-RAY DIFFRACTION4chain 'A' and (resid 386 through 398 )A386 - 398
5X-RAY DIFFRACTION5chain 'A' and (resid 399 through 468 )A399 - 468

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