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Yorodumi- PDB-5mdp: Crystal structure of in vitro folded Chitoporin VhChip from Vibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mdp | ||||||
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Title | Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form II) | ||||||
Components | Chitoporin | ||||||
Keywords | SUGAR BINDING PROTEIN / outer membrane protein / Vibrio harveyi / porin channel | ||||||
Function / homology | Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / Chitoporin Function and homology information | ||||||
Biological species | Vibrio harveyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Zahn, M. / van den Berg, B. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for chitin acquisition by marine Vibrio species. Authors: Aunkham, A. / Zahn, M. / Kesireddy, A. / Pothula, K.R. / Schulte, A. / Basle, A. / Kleinekathofer, U. / Suginta, W. / 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 | 5mdp.cif.gz | 403.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mdp.ent.gz | 336.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdp ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdp | HTTPS FTP |
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-Related structure data
Related structure data | 5mdoSC 5mdqC 5mdrC 5mdsC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 10 - 350 / Label seq-ID: 12 - 352
NCS ensembles :
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-Components
#1: Protein | Mass: 39192.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0 |
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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: 4.31 Å3/Da / Density % sol: 71.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28% (w/v) PEG 400, 0.5 M potassium iodide, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→29.21 Å / Num. obs: 34933 / % possible obs: 95.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.1 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.08→3.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.385 / % possible all: 38.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MDO Resolution: 3.08→127.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 50.469 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R: 1.766 / ESU R Free: 0.374 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.514 Å2
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Refinement step | Cycle: 1 / Resolution: 3.08→127.2 Å
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Refine LS restraints |
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