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Yorodumi- PDB-2ynk: Wzi, an Outer Membrane Protein Involved in Group 1 Capsule Assemb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ynk | ||||||
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Title | Wzi, an Outer Membrane Protein Involved in Group 1 Capsule Assembly in Escherichia coli, is a Carbohydrate Binding Beta-Barrel | ||||||
Components | WZI | ||||||
Keywords | MEMBRANE PROTEIN / CAPSULE EXPORT | ||||||
Function / homology | Function and homology information Capsule assembly protein Wzi / Capsule assembly protein Wzi / Capsule assembly protein Wzi superfamily / Capsule assembly protein Wzi / Porin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å | ||||||
Authors | Bushell, S.R. / Mainprize, I.L. / Wear, M.A. / Lou, H. / Kong, L. / Davis, B. / Bayley, H. / Whitfield, C. / Naismith, J.H. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Wzi is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia Coli. Authors: Bushell, S.R. / Mainprize, I.L. / Wear, M.A. / Lou, H. / Whitfield, C. / Naismith, J.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ynk.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ynk.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ynk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2ynk ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2ynk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51089.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: B44 / References: UniProt: Q8GNN6 | ||||||
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#2: Chemical | ChemComp-OCT / #3: Chemical | ChemComp-D12 / #4: Chemical | ChemComp-HEX / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.61 % / Description: NONE |
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Crystal grow | Details: SEE PAPER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97862 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 31, 2010 / Details: TOROIDAL FOCUSSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL-CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→59.37 Å / Num. obs: 28226 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.64→2.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.64→59.37 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.887 / SU B: 23.784 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.671 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→59.37 Å
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