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Yorodumi- PDB-5tgi: Structure of the SNX5 PX domain in complex with chlamydial protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tgi | ||||||||||||
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Title | Structure of the SNX5 PX domain in complex with chlamydial protein IncE in space group P212121 | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / host-pathogen endosome | ||||||||||||
Function / homology | Function and homology information retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Chlamydia trachomatis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||||||||
Authors | Collins, B. / Paul, B. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: To Be Published Title: Structure of the SNX5 PX domain in complex with chlamydial protein IncE Authors: Collins, B. / Paul, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tgi.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tgi.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/5tgi ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tgi | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 17357.504 Da / Num. of mol.: 2 / Fragment: UNP residues 22-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3 #2: Protein/peptide | Mass: 2306.615 Da / Num. of mol.: 2 / Fragment: UNP residues 111-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incE / Production host: Escherichia coli (E. coli) / 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: 2.3 Å3/Da / Density % sol: 46.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M KSCN, 25% PEG 2K MME, 100 mM sodium acetate (pH 5.5) |
-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: 1.98→60.7 Å / Num. obs: 26075 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.868 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→45.151 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→45.151 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.3472 Å / Origin y: 26.5329 Å / Origin z: -19.9468 Å
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Refinement TLS group | Selection details: all |