+Open data
-Basic information
Entry | Database: PDB / ID: 2wjq | ||||||
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Title | NanC porin structure in hexagonal crystal form. | ||||||
Components | PROBABLE N-ACETYLNEURAMINIC ACID OUTER MEMBRANE CHANNEL PROTEIN NANC | ||||||
Keywords | TRANSPORT PROTEIN / KDGM FAMILY / BETA-BARREL / MONOMERIC PORIN / OUTER MEMBRANE PROTEIN / SIALIC ACID TRANSLOCATION | ||||||
Function / homology | Function and homology information oligosaccharide transport / sialic acid transmembrane transporter activity / oligosaccharide transporting porin 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 / MIRAS / Resolution: 2 Å | ||||||
Authors | Wirth, C. / Condemine, G. / Schirmer, T. / Peneff, C.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Nanc Crystal Structure, a Model for Outer Membrane Channels of the Acidic Sugar-Specific Kdgm Porin Family. Authors: Wirth, C. / Condemine, G. / Boiteux, C. / Berneche, S. / Schirmer, T. / Peneff, C.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-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 | 2wjq.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wjq.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/2wjq ftp://data.pdbj.org/pub/pdb/validation_reports/wj/2wjq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25489.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PKSM717 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)OMP8/PLYS / References: UniProt: P69856 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-OCT / #4: Chemical | ChemComp-LDA / #5: Water | ChemComp-HOH / | Nonpolymer details | N-OCTANE (OCT): OCT ARE INCOMPLETE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: 5-10% ISOPROPANOL, 0.15M CACL2, 0.1M ACETATE PH 4.6, VAPOR DIFFUSION, 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22890 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.2 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 43 TO 52 HAVE NOT BEEN MODELED DUE TO MISSING DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.728 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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