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Yorodumi- PDB-4fch: Crystal Structure SusE from Bacteroides thetaiotaomicron with mal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fch | |||||||||
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Title | Crystal Structure SusE from Bacteroides thetaiotaomicron with maltoheptaose | |||||||||
Components | Outer membrane protein SusE | |||||||||
Keywords | Carbohydrate-binding protein / starch binding / outermembrane / extracellular | |||||||||
Function / homology | Function and homology information starch catabolic process / starch binding / outer membrane / cell outer membrane Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Koropatkin, N.M. / Cameron, E.A. / Martens, E.C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism. Authors: Cameron, E.A. / Maynard, M.A. / Smith, C.J. / Smith, T.J. / Koropatkin, N.M. / Martens, E.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fch.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fch.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fch_validation.pdf.gz | 873.8 KB | Display | wwPDB validaton report |
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Full document | 4fch_full_validation.pdf.gz | 878.2 KB | Display | |
Data in XML | 4fch_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4fch_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fch ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fch | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24756.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3700, susE / Plasmid: pET-28TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: G8JZT0 #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: 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: 2.97 Å3/Da / Density % sol: 58.62 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis Tris Propane, 2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2011 / Details: mirrors |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 141909 / Num. obs: 141909 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.084 / Net I/σ(I): 39.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4 / Num. unique all: 6557 / Rsym value: 0.301 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet SusE Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.2 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.954 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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