+Open data
-Basic information
Entry | Database: PDB / ID: 1s46 | ||||||
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Title | Covalent intermediate of the E328Q amylosucrase mutant | ||||||
Components | amylosucrase | ||||||
Keywords | TRANSFERASE / protein-glucopyranosyl covalent intermediate / (beta/alpha)8-barrel | ||||||
Function / homology | Function and homology information amylosucrase / amylosucrase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Neisseria polysaccharea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jensen, M.H. / Mirza, O. / Albenne, C. / Remaud-Simeon, M. / Monsan, P. / Gajhede, M. / Skov, L.K. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal structure of the covalent intermediate of amylosucrase from Neisseria polysaccharea. Authors: Jensen, M.H. / Mirza, O. / Albenne, C. / Remaud-Simeon, M. / Monsan, P. / Gajhede, M. / Skov, L.K. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Amylosucrase, a Glucan-Synthesizing Enzyme from the Alpha-Amylase Family Authors: Skov, L.K. / Mirza, O. / Henriksen, A. / De Montalk, G.P. / Remaud-Simeon, M. / Sarcabal, P. / Willemot, R.M. / Monsan, P. / Gajhede, M. #2: Journal: Biochemistry / Year: 2001 Title: Crystal Structure Of Amylosucrase From Neisseria Polysaccharea In Complex With D-Glucose Authors: Mirza, O. / Skov, L.K. / Remaud-Simeon, M. / De Montalk, G.P. / Albenne, C. / Monsan, P. / Gajhede, M. | ||||||
History |
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Remark 999 | SEQUENCE THE DISCREPANCY BETWEEN RESIDUE TYR 131 AND THE GENBANK SEQUENCE DATABASE REFERENCE, ... SEQUENCE THE DISCREPANCY BETWEEN RESIDUE TYR 131 AND THE GENBANK SEQUENCE DATABASE REFERENCE, ACCESSION 4107260, RESIDUE HIS 139 IS DUE TO A PCR ERROR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s46.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s46.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s46_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 1s46_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 1s46_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1s46_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s46 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s46 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 71530.086 Da / Num. of mol.: 1 / Mutation: E328Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria polysaccharea (bacteria) / Plasmid: pGEX-6-P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9ZEU2, amylosucrase |
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#2: Sugar | ChemComp-BGC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sucrose, PEG 6000, SODIUM CHLORIDE, TRIS-HCL, EDTA, HEPES, DTT, Alpha-D-glucopyranosyl fluoride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.011 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2000 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 32544 / Num. obs: 32544 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.081 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6 / Num. unique all: 3287 / Rsym value: 0.328 / % possible all: 94.7 |
Reflection | *PLUS Num. measured all: 128590 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.328 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 844885.82 / 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: 10 Å2 / ksol: 0.318055 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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