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- PDB-1k46: Crystal Structure of the Type III Secretory Domain of Yersinia Yo... -

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Basic information

Entry
Database: PDB / ID: 1k46
TitleCrystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer
ComponentsPROTEIN-TYROSINE PHOSPHATASE YOPH
KeywordsHYDROLASE / domain-swap / phosphopeptide-binding domain / type III secretion domain
Function / homology
Function and homology information


dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal 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, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain ...YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal 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, 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsSmith, C.L. / Khandelwal, P. / Keliikuli, K. / Zuiderweg, E.R.P. / Saper, M.A.
Citation
Journal: Mol.Microbiol. / Year: 2001
Title: Structure of the type III secretion and substrate-binding domain of Yersinia YopH phosphatase.
Authors: Smith, C.L. / Khandelwal, P. / Keliikuli, K. / Zuiderweg, E.R. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Identification of Residues in the N-terminal Domain of the Yersinia Tyrosine Phosphatase that are Critical for Substrate Recognition
Authors: Montagna, L.G. / Ivanov, M.I. / Bliska, J.B.
#2: Journal: Mol.Microbiol. / Year: 1998
Title: Identification of an Amino-terminal Substrate-binding Domain in the Yersinia Tyrosine Phosphatase that is Required for Efficient Recognition of Focal Adhesion Targets
Authors: Black, D.S. / Montagna, L.G. / Zitsmann, S. / Bliska, J.B.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THIS IS LIKELY THE BIOLOGICALLY-RELEVANT STRUCTURE. THE RELEVANCE OF THE DOMAIN-SWAPPED DIMER OBSERVED IN THE CRYSTAL STRUCTURE IS DESCRIBED IN THE JRNL REFERENCE. ALSO SEE REMARK 900. THE OTHER MOLECULE OF THE DOMAIN-SWAPPED DIMER IS GENERATED BY APPLYING CRYSTALLOGRAPHIC OPERATOR 3 IN REMARK 290 FOLLOWED BY A TRANSLATION OF 47.90 IN X.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE YOPH


Theoretical massNumber of molelcules
Total (without water)14,8831
Polymers14,8831
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN-TYROSINE PHOSPHATASE YOPH

A: PROTEIN-TYROSINE PHOSPHATASE YOPH


Theoretical massNumber of molelcules
Total (without water)29,7652
Polymers29,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5070 Å2
ΔGint-34 kcal/mol
Surface area12080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.900, 120.700, 48.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsYopH(1-129) can exist as a monomer or dimer in solution. Crystal structure is a domain-swapped dimer consisting of two molecules related by a crystallographic two fold axis: -x+1,y,-z+1/2. The physiologically-relevant form is likely the monomer.

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE YOPH / YopH phosphatase


Mass: 14882.599 Da / Num. of mol.: 1 / Fragment: amino-terminal domain (residues 1-129)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: yopH / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08538, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, sodium chlolride, Tris , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropNaCl
21 mMEDTA1drop
30.1 %beta-mercaptoethanol1drop
410 mMimidazole1droppH7.2
510 mg/mlprotein1drop
62-10 %PEG80001reservoir
790-100 mM1reservoirNaCl
8100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 1998 / Details: mirrors
RadiationMonochromator: Yale double focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22 Å / Num. all: 7503 / Num. obs: 7503 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 16.2 / Num. unique all: 720 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 68285 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 720

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: de novo

Resolution: 2.2→22 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 747 -random
Rwork0.224 ---
all-7479 --
obs-7479 100 %-
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 110 1054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.115
LS refinement shellResolution: 2.2→2.25 Å
RfactorNum. reflection
Rfree0.2757 49
Rwork0.222 -
obs-461
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22 Å / σ(F): 0 / Rfactor obs: 0.224 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
LS refinement shell
*PLUS
Rfactor Rwork: 0.222 / Rfactor obs: 0.222

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