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Yorodumi- PDB-3gbd: Crystal structure of the isomaltulose synthase SmuA from Protamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gbd | ||||||
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Title | Crystal structure of the isomaltulose synthase SmuA from Protaminobacter rubrum | ||||||
Components | Sucrose isomerase SmuA from Protaminobacter rubrum | ||||||
Keywords | ISOMERASE / sucrose isomerase / glycoside hydrolase / Protaminobacter rubrum | ||||||
Function / homology | Function and homology information isomaltulose synthase / isomaltulose synthase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Protaminobacter rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ravaud, S. / Robert, X. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: Febs Lett. / Year: 2009 Title: Structural determinants of product specificity of sucrose isomerases Authors: Ravaud, S. / Robert, X. / Watzlawick, H. / Haser, R. / Mattes, R. / Aghajari, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gbd.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbd.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gbd_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 3gbd_full_validation.pdf.gz | 462.4 KB | Display | |
Data in XML | 3gbd_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 3gbd_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbd ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbd | HTTPS FTP |
-Related structure data
Related structure data | 3gbeC 1m53S 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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Unit cell |
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-Components
#1: Protein | Mass: 65688.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Protaminobacter rubrum (bacteria) / Strain: CBS 547.77 / Gene: smuA / Plasmid: pHWG314 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: D0VX20*PLUS, isomaltulose synthase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-FLC / | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M tri-Li-citrate, 20% PEG3350, pH7, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9803 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2004 / Details: mirrors |
Radiation | Monochromator: synchrotron mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9803 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.9 Å / Num. obs: 51963 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.95→2.05 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.315 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M53 Resolution: 1.95→19.89 Å / Rfactor Rfree error: 0.0003 / Data cutoff high absF: 2590194.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.4823 Å2 / ksol: 0.333264 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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