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Yorodumi- PDB-6e8r: Structure of the SNX32 PX domain in complex with Chlamydial prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e8r | |||||||||
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Title | Structure of the SNX32 PX domain in complex with Chlamydial protein IncE in space group I121 | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / PX domain | |||||||||
Function / homology | Function and homology information retrograde transport, endosome to Golgi / regulation of macroautophagy / phosphatidylinositol binding / protein transport / endosome / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Chlamydia trachomatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.268 Å | |||||||||
Authors | Paul, B. / Collins, B. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To be Published Title: Crystal structure of the SNX32 PX domain in complex with the Chlamydia trachomatis inclusion protein IncE Authors: Paul, B. / Collins, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e8r.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e8r.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 6e8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e8r_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 6e8r_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 6e8r_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6e8r_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e8r ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e8r | HTTPS FTP |
-Related structure data
Related structure data | 5tgiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17353.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX32, SNX6B / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XE0 #2: Protein/peptide | Mass: 2588.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incE / Production host: synthetic construct (others) / References: UniProt: B7SCI5 #3: 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: 3.65 Å3/Da / Density % sol: 66.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 8000, 0.1 M TRIS (pH 8.0), 0.01 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.268→43.767 Å / Num. obs: 25107 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.176 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.268→2.34 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2222 / CC1/2: 0.726 / Rpim(I) all: 0.54 / Rrim(I) all: 1.046 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TGI Resolution: 2.268→43.767 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.268→43.767 Å
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Refine LS restraints |
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LS refinement shell |
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