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- PDB-4zi4: YopH W354H Yersinia enterocolitica PTPase bond with Divanadate gl... -

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Basic information

Entry
Database: PDB / ID: 4zi4
TitleYopH W354H Yersinia enterocolitica PTPase bond with Divanadate glycerol ester in the active site
ComponentsTyrosine-protein phosphatase YopH
KeywordsHYDROLASE / phosphatase / Yersinia / PTP
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Divanadate Glycerol ester / VANADATE ION / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.121 Å
AuthorsMoise, G.E. / Johnson, S.J. / Hengge, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM47297 United States
Citation
Journal: Biochemistry / Year: 2015
Title: Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites.
Authors: Moise, G. / Gallup, N.M. / Alexandrova, A.N. / Hengge, A.C. / Johnson, S.J.
#1: Journal: To Be Published
Title: Locked WPD-loops and divanadate esters in two new tryptophan mutants of the protein-tyrosine phosphatase YopH
Authors: Moise, G.E. / Johnson, S.J. / Hengge, A.C.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Tyrosine-protein phosphatase YopH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8973
Polymers33,5061
Non-polymers3912
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.888, 60.512, 89.358
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 Tyrosine-protein phosphatase YopH / Virulence protein


Mass: 33505.820 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 164-468) / Mutation: C235R, W354H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: DH5a / Gene: yopH, yop51 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Chemical ChemComp-DVG / Divanadate Glycerol ester


Mass: 275.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10O8V2
#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.: 392 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Peg 3350, HEPES / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 98 K / Ambient temp details: under liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 109639 / % possible obs: 99.4 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 52.8
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 10.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
AUTOMARdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPT

1ypt


Resolution: 1.121→26.262 Å / FOM work R set: 0.931 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 5493 5.01 %random
Rwork0.1409 104056 --
obs0.1418 109549 99.18 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.844 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso max: 60.97 Å2 / Biso mean: 20.01 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.7681 Å2-0 Å20 Å2
2---2.9725 Å20 Å2
3---0.2044 Å2
Refinement stepCycle: final / Resolution: 1.121→26.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 26 392 2580
Biso mean--21.24 34.67 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082329
X-RAY DIFFRACTIONf_angle_d1.2913177
X-RAY DIFFRACTIONf_chiral_restr0.076365
X-RAY DIFFRACTIONf_plane_restr0.006425
X-RAY DIFFRACTIONf_dihedral_angle_d12.625937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1208-1.13350.26651970.22783067326490
1.1335-1.14690.21311700.204834783648100
1.1469-1.16090.19821870.177434143601100
1.1609-1.17560.17531820.161734893671100
1.1756-1.1910.19151750.153134403615100
1.191-1.20730.17821810.14434743655100
1.2073-1.22460.1721940.134134203614100
1.2246-1.24290.15831710.130834653636100
1.2429-1.26230.17461960.127634523648100
1.2623-1.2830.14451800.122134813661100
1.283-1.30510.13891460.111734833629100
1.3051-1.32880.14911950.11134453640100
1.3288-1.35440.13632040.106234583662100
1.3544-1.3820.15362010.108234783679100
1.382-1.41210.12491630.110634763639100
1.4121-1.44490.15051760.110534863662100
1.4449-1.48110.13291680.106635023670100
1.4811-1.52110.14481830.107135103693100
1.5211-1.56590.12951780.10734623640100
1.5659-1.61640.12361560.106735253681100
1.6164-1.67410.12781830.111735093692100
1.6741-1.74120.16021990.117734803679100
1.7412-1.82040.13831730.122635323705100
1.8204-1.91630.14911870.125934963683100
1.9163-2.03640.13491960.124235213717100
2.0364-2.19350.12351910.122535093700100
2.1935-2.41410.13972020.126835363738100
2.4141-2.76310.16461870.142735653752100
2.7631-3.480.1491920.158135923784100
3.48-26.26940.22371800.1923311349188

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