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Yorodumi- PDB-3r9v: Cocrystal Structure of Proteolytically Truncated Form of IpaD fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r9v | ||||||
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Title | Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate | ||||||
Components | Invasin ipaD | ||||||
Keywords | CELL INVASION / type III secretion system / tip protein / deoxycholate | ||||||
Function / homology | Function and homology information effector-mediated activation of programmed cell death in host / extracellular region Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Barta, M.L. / Dickenson, N.E. / Picking, W.L. / Picking, W.D. / Geisbrecht, B.V. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Identification of the bile salt binding site on IpaD from Shigella flexneri and the influence of ligand binding on IpaD structure. Authors: Barta, M.L. / Guragain, M. / Adam, P. / Dickenson, N.E. / Patil, M. / Geisbrecht, B.V. / Picking, W.L. / Picking, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r9v.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r9v.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r9v_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3r9v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3r9v_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3r9v_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/3r9v ftp://data.pdbj.org/pub/pdb/validation_reports/r9/3r9v | HTTPS FTP |
-Related structure data
Related structure data | 2j0oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31659.391 Da / Num. of mol.: 2 / Fragment: unp residues 39-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013 #2: Chemical | #3: Chemical | #4: 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: 2.02 Å3/Da / Density % sol: 39.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02M magnesium chloride hexahydrate, 0.1M HEPES, 22% (w/v) Poly(acrylic acid sodium salt) 5100, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2010 |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45 Å / Num. all: 40352 / Num. obs: 39424 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.072 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.47 / Rsym value: 0.451 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J0O Resolution: 1.9→25.283 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.141 Å2 / ksol: 0.336 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.283 Å
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Refine LS restraints |
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LS refinement shell |
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