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Yorodumi- PDB-1ttw: Crystal structure of the Yersinia Pestis type III secretion chape... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ttw | ||||||
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Title | Crystal structure of the Yersinia Pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2 | ||||||
Components |
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Keywords | CHAPERONE / type III secretion | ||||||
Function / homology | Function and homology information protein secretion by the type III secretion system / : / protein tyrosine phosphatase activity Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.38 Å | ||||||
Authors | Phan, J. / Tropea, J.E. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2. Authors: Phan, J. / Tropea, J.E. / 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 | 1ttw.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ttw.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1ttw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/1ttw ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1ttw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15454.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ARG9, UniProt: Q7BTX0*PLUS |
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#2: Protein | Mass: 6540.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: GenBank: 28373010, UniProt: Q93KQ4*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: 1.8 M ammonium sulphate, 200 mM magnesium acetate, 100 mM CAPSO, 2% dioxane, 1.6 mM CHAPS, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98397 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 22, 2003 |
Radiation | Monochromator: Insertion Device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98397 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→25 Å / Num. all: 9196 / Num. obs: 7916 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 66.026 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.38→2.48 Å / Redundancy: 10 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4 / Num. unique all: 888 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.38→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.627 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.31 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.441 Å / Total num. of bins used: 20 /
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