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- PDB-1l2w: Crystal Structure of the Yersinia Virulence Effector YopE Chapero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l2w | ||||||
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Title | Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE | ||||||
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![]() | CHAPERONE / CHAPERONE AND VIRULENCE PROTEIN | ||||||
Function / homology | ![]() protein secretion by the type III secretion system / negative regulation of phagocytosis / regulation of protein secretion / : / GTPase activator activity / cell outer membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Birtalan, S.C. / Phillips, R.M. / Ghosh, P. | ||||||
![]() | ![]() Title: Three-dimensional secretion signals in chaperone-effector complexes of bacterial pathogens. Authors: Birtalan, S.C. / Phillips, R.M. / Ghosh, P. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-H, MATCHES SWISS PROT ENTRY P31491, WHOSE ...SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-H, MATCHES SWISS PROT ENTRY P31491, WHOSE SOURCE IS YERSINIA PESTIS. THE SOURCE OF THE SYCE PROTEIN IN THIS ENTRY IS YERSINIA PSEUDOTUBERCULOSIS. THERE IS AN EXTRA GLYCINE, RESIDUE 1, IN CHAINS A-H WHICH WAS INSERTED FOR CLONING PURPOSES, and the last 8 residues were cleaved to yield residues 0-122. The N- and C- terminal residues of chains I-L were cleaved to yield residues 17-85. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.6 KB | Display | ![]() |
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PDB format | ![]() | 196.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 525.2 KB | Display | ![]() |
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Full document | ![]() | 552 KB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jyaS S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13843.607 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7277.952 Da / Num. of mol.: 4 / Fragment: Chaperone-binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 8000, sodium tartrate, sodium acetate, dithiothreitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→20 Å / Num. all: 87145 / Num. obs: 84804 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 36.69 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 18.22 |
Reflection shell | Resolution: 1.99→2.03 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.77 / Num. unique all: 4425 / Rsym value: 0.46 / % possible all: 96.5 |
Reflection | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 20 Å / % possible obs: 96.7 % |
Reflection shell | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 2.07 Å / % possible obs: 96.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1jya Resolution: 2→20 Å / Isotropic thermal model: atomic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 48.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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Refinement | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 20 Å / Num. reflection obs: 77053 / Num. reflection Rfree: 4091 / % reflection Rfree: 5 % / Rfactor obs: 0.249 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.249 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3497 |