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Yorodumi- PDB-1hy5: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF YOPE-YERSINIA PESTIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hy5 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF YOPE-YERSINIA PESTIS GAP EFFECTOR PROTEIN. | ||||||
Components | YERSINIA PESTIS VIRULENCE PROTEIN YOPE | ||||||
Keywords | TOXIN / four helix up-down-up-down antiparallel bundle / beta hairpin / arginine finger | ||||||
Function / homology | Function and homology information negative regulation of phagocytosis / : / GTPase activator activity / cell outer membrane Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.25 Å | ||||||
Authors | Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Crystal structure of the Yersinia pestis GTPase activator YopE. Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hy5.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hy5.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/1hy5 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/1hy5 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | biological assembly is a monomer - crystal AU contains a dimer. RMSD of the Ca positions within the dimer is 0.34 A |
-Components
#1: Protein | Mass: 14764.720 Da / Num. of mol.: 2 Fragment: C-TERMINAL DOMAIN (RESIDUES 90-219); BACTERIAL GTPASE ACTIVATING PROTEIN (GAP DOMAIN) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YOPE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)DE3 / References: UniProt: P31493 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.84 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Ammonium sulphate, bicine, potassium nitrate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 5, 2000 / Details: osmic mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→100 Å / Num. all: 22062 / Num. obs: 18478 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / Num. unique all: 2291 / % possible all: 96.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 22062 / % possible obs: 98.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 96.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→100 Å Isotropic thermal model: isotropic individual atomic B factors Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh-Huber Details: Refinement on unmerged Friedel opposites (due to small but tangible selenium anomalous contribution). Refinement by conjugated-gradient least-squares. Selenomethionine restraints derived ...Details: Refinement on unmerged Friedel opposites (due to small but tangible selenium anomalous contribution). Refinement by conjugated-gradient least-squares. Selenomethionine restraints derived from Hic-Up. Two monomers were restrained by NCS (1,4-restraints generated by NCSY in SHELXL). Removal of the NCS restraints does not result in significant changes in the model. The structure was refined using home data (wavelength 1.5418).
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Solvent computation | Solvent model: Babinet (SHELXL) / Bsol: 250.018 Å2 / ksol: 0.879 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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