+Open data
-Basic information
Entry | Database: PDB / ID: 7vu1 | ||||||
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Title | Chitoporin from Escherichia coli complex with chitohexaose | ||||||
Components | Chitoporin | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein Chitoporin specific porin | ||||||
Function / homology | Function and homology information diacetylchitobiose metabolic process / oligosaccharide transport / polysaccharide transport / channel activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Suginta, W. / Soysa, H.S.M. / Amornloetwattana, R. / van den Berg, B. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Chitporin from Escherichia coli complex with chitohexaose Authors: Soysa, H.S.M. / Suginta, W. / Amornloetwattana, R. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vu1.cif.gz | 445.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vu1.ent.gz | 297.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/7vu1 ftp://data.pdbj.org/pub/pdb/validation_reports/vu/7vu1 | HTTPS FTP |
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-Related structure data
Related structure data | 7vtzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49512.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: chiP, ybfM, b0681, JW0667 / Production host: Escherichia coli (E. coli) / References: UniProt: P75733 |
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-Sugars , 2 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-DMU / |
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-Non-polymers , 3 types, 467 molecules
#4: Chemical | ChemComp-C8E / ( #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.49 Å3/Da / Density % sol: 64.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30-35% PEG 400, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97883 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97883 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62.5 Å / Num. obs: 107599 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.85 Å2 / CC1/2: 0.974 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 5303 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VTZ Resolution: 1.9→62.34 Å / SU ML: 0.2073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0807 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→62.34 Å
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Refine LS restraints |
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LS refinement shell |
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