+Open data
-Basic information
Entry | Database: PDB / ID: 3ck8 | |||||||||
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Title | B. thetaiotaomicron SusD with beta-cyclodextrin | |||||||||
Components | SusDLunca, Bihor | |||||||||
Keywords | SUGAR BINDING PROTEIN / TPR repeat / carbohydrate binding / starch binding | |||||||||
Function / homology | Function and homology information starch metabolic process / starch catabolic process / starch binding / outer membrane / cell outer membrane / calcium ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | |||||||||
Authors | Koropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J. | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Authors: Koropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ck8.cif.gz | 238.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ck8.ent.gz | 186 KB | Display | PDB format |
PDBx/mmJSON format | 3ck8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3ck8 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3ck8 | HTTPS FTP |
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-Related structure data
Related structure data | 3ck7C 3ck9SC 3ckbC 3ckcC C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 59783.340 Da / Num. of mol.: 2 / Fragment: UNP residues 26-551 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: SusD / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A1G2 #2: Polysaccharide | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON UNIVERSITY (FROM JEFFREY I GORDON'S ...THE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON | |
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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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 298 K / Method: seeding in batch / pH: 6 Details: 50mM sodium cacodylate, 75mM Calcium acetate, 14% PEG 8000, 10mM beta-cyclodextrin, pH 6.0, seeding in batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Sep 1, 2007 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→60.2 Å / Num. all: 66380 / Num. obs: 66380 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.033 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 8307 / Rsym value: 0.073 / % possible all: 82.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3CK9 Resolution: 2.1→60.19 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.241 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.416 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→60.19 Å
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Refine LS restraints |
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Xplor file |
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