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- PDB-1k46: Crystal Structure of the Type III Secretory Domain of Yersinia Yo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k46 | ||||||
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Title | Crystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer | ||||||
![]() | PROTEIN-TYROSINE PHOSPHATASE YOPH | ||||||
![]() | HYDROLASE / domain-swap / phosphopeptide-binding domain / type III secretion domain | ||||||
Function / homology | ![]() dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Smith, C.L. / Khandelwal, P. / Keliikuli, K. / Zuiderweg, E.R.P. / Saper, M.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Remark 300 | BIOMOLECULE: 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.2 KB | Display | ![]() |
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PDB format | ![]() | 26.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
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Full document | ![]() | 427.4 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | YopH(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 | 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.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 1998 / Details: mirrors |
Radiation | Monochromator: Yale double focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() 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
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Displacement parameters | Biso mean: 30.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å
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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 |