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Yorodumi- PDB-5mdq: Crystal structure of outer membrane expressed Chitoporin VhChip f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mdq | ||||||
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Title | Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi | ||||||
Components | Chitoporin | ||||||
Keywords | SUGAR BINDING PROTEIN / outer membrane protein Vibrio harveyi porin channel | ||||||
Function / homology | Function and homology information porin activity / monoatomic ion transmembrane transport / cell outer membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio harveyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 5mdq.cif.gz | 415.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mdq.ent.gz | 346 KB | Display | PDB format |
PDBx/mmJSON format | 5mdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mdq_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 5mdq_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 5mdq_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 5mdq_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdq ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdq | HTTPS FTP |
-Related structure data
Related structure data | 5mdoSC 5mdpC 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: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 350 / Label seq-ID: 1 - 350
NCS ensembles :
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-Components
#1: Protein | Mass: 38535.668 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 #2: Chemical | #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: 4.45 Å3/Da / Density % sol: 72.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28% (w/v) PEG 400, 0.2 M sodium acetate, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.15 Å / Num. obs: 66687 / % possible obs: 95.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.078 / Net I/σ(I): 12.2 |
Reflection shell | Redundancy: 4.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.1 / Rpim(I) all: 0.58 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MDO Resolution: 2.5→128.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.921 / SU B: 22.653 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.22 / 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: 55.574 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→128.39 Å
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Refine LS restraints |
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