+Open data
-Basic information
Entry | Database: PDB / ID: 3k8l | |||||||||
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Title | Crystal structure of SusG-D498N mutant with maltoheptaose | |||||||||
Components | Alpha-amylase, susG | |||||||||
Keywords | MEMBRANE PROTEIN / amylase / alpha8/beta8 barrel / CBM / beta-sandwich | |||||||||
Function / homology | Function and homology information starch catabolic process / starch binding / alpha-amylase / outer membrane / oligosaccharide catabolic process / alpha-amylase activity / cell outer membrane / calcium ion binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Koropatkin, N.M. / Smith, T.J. | |||||||||
Citation | Journal: Structure / Year: 2010 Title: SusG: A Unique Cell-Membrane-Associated alpha-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules. Authors: Koropatkin, N.M. / 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 | 3k8l.cif.gz | 287.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k8l.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k8l_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3k8l_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 3k8l_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 3k8l_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/3k8l ftp://data.pdbj.org/pub/pdb/validation_reports/k8/3k8l | HTTPS FTP |
-Related structure data
Related structure data | 3k8kSC 3k8mC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 75310.883 Da / Num. of mol.: 2 / Mutation: D498N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_3698, SusG / Plasmid: pET-28rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A1G3 |
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-Sugars , 3 types, 6 molecules
#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)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | #4: Polysaccharide | |
-Non-polymers , 3 types, 546 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-EDO / #7: 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: 3.55 Å3/Da / Density % sol: 65.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mM maltoheptaose, 0.5mM CaCl2, 19% PEG 4000, 100mM LiSO4, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 30, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→500 Å / Num. obs: 98589 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.061 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 4050 / Rsym value: 0.177 |
-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 3K8K Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 23.364 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.71 Å2 / Biso mean: 33.45 Å2 / Biso min: 10.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Xplor file |
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