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Open data
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Basic information
Entry | Database: PDB / ID: 7eqm | ||||||
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Title | Apo Truncated VhChiP (Delta 1-19) | ||||||
![]() | Chitoporin | ||||||
![]() | TRANSPORT PROTEIN / Vibrio species / Chitin / outer-membrane protein / sugar-specific porin / marine bacteria | ||||||
Function / homology | Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / monoatomic ion transmembrane transport / cell outer membrane / metal ion binding / Chitoporin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aunkham, A. / Sanram, S. / Suginta, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and functionof truncated VhChiP Authors: Aunkham, A. / Sanram, S. / Suginta, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.4 KB | Display | ![]() |
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PDB format | ![]() | 168.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.2 MB | Display | ![]() |
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Full document | ![]() | 6.2 MB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 55.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mdoS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36469.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-C8E / ( #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.21 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M Lithium sulfate, 0.1 M ADA pH 5.2, and 26% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2020 Details: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20.0033313589 Å / Num. obs: 43095 / % possible obs: 89.3637 % / Redundancy: 3.1 % / Biso Wilson estimate: 31.8229899268 Å2 / CC1/2: 0.868 / CC star: 0.964 / Rpim(I) all: 0.061 / Rrim(I) all: 0.119 / Χ2: 0.934 / Net I/av σ(I): 7.3 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.5→7.98 Å / Num. unique obs: 43095 / CC1/2: 0.911 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MDO Resolution: 2.50002374963→20.0033313589 Å / SU ML: 0.281487800061 / Cross valid method: NONE / σ(F): 1.37519310272 / Phase error: 23.5731369938 Stereochemistry target values: GeoStd + Monomer Library + 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: 33.0130337587 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.50002374963→20.0033313589 Å
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Refine LS restraints |
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LS refinement shell |
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