+Open data
-Basic information
Entry | Database: PDB / ID: 2wvp | ||||||
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Title | Synthetically modified OmpG | ||||||
Components | OUTER MEMBRANE PROTEIN G | ||||||
Keywords | MEMBRANE PROTEIN / ION-CHANNEL ENGINEERING / OMPG HYBRIDS | ||||||
Function / homology | Function and homology information carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Grosse, W. / Reiss, P. / Reitz, S. / Cebi, M. / Luebben, W. / Koert, U. / Essen, L.-O. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Structural and Functional Characterization of a Synthetically Modified Ompg. Authors: Grosse, W. / Reiss, P. / Reitz, S. / Cebi, M. / Luebben, W. / Koert, U. / Essen, L.-O. | ||||||
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 | 2wvp.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvp.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 2wvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wvp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2wvp_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2wvp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2wvp_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvp ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvp | HTTPS FTP |
-Related structure data
Related structure data | 2f1cS S: Starting model for refinement |
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Similar 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: 33574.172 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: Y209C MUTANT CHEMICALLY MODIFIED WITH N-(2-ETHYL-IODO-ACETAMIDE)-DANSYL Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) OMP9 / References: UniProt: P76045 | ||||||||
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#2: Chemical | ChemComp-420 / | ||||||||
#3: Chemical | ChemComp-C8E / ( #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | N-OCTYLTETRAOXYETHYLENE (EDO): PARTIAL ELECTRON DENSITY OF N-OCTYLTETRAOXYETHYLENE WAS MODELED WITH ...N-OCTYLTETRA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.61 % / Description: NONE |
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Crystal grow | pH: 5.75 Details: 50 MM CACODYLATE, PH 5.75, 1.2 M SODIUM FORMATE AND 28% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 15345 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.2 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F1C Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 21.587 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE ONLY. U VALUES HAVE BEEN REFINED RESIDUAL ONLY. THERE ARE THREE GAPS IN DISORDERED LOOPS ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU ...Details: HYDROGENS HAVE BEEN ADDED IN THE ONLY. U VALUES HAVE BEEN REFINED RESIDUAL ONLY. THERE ARE THREE GAPS IN DISORDERED LOOPS ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.306 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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