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Yorodumi- PDB-1jgi: Crystal Structure of the Active Site Mutant Glu328Gln of Amylosuc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jgi | |||||||||
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Title | Crystal Structure of the Active Site Mutant Glu328Gln of Amylosucrase from Neisseria polysaccharea in Complex with the Natural Substrate Sucrose | |||||||||
Components | amylosucrase | |||||||||
Keywords | TRANSFERASE / active site mutant Glu328Gln / sucrose complex | |||||||||
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 Å | |||||||||
Authors | Mirza, O. / Skov, L.K. / Gajhede, M. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structures of amylosucrase from Neisseria polysaccharea in complex with D-glucose and the active site mutant Glu328Gln in complex with the natural substrate sucrose. Authors: Mirza, O. / Skov, L.K. / Remaud-Simeon, M. / Potocki de Montalk, G. / Albenne, C. / Monsan, P. / Gajhede, M. | |||||||||
History |
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Remark 999 | SEQUENCE THE DISCREPANCY BETWEEN RESIDUES TYR 131 & ASP 537 AND THE GENBANK SEQUENCE DATABASE ...SEQUENCE THE DISCREPANCY BETWEEN RESIDUES TYR 131 & ASP 537 AND THE GENBANK SEQUENCE DATABASE REFERENCE, ACCESSION 4107260, RESIDUES HIS 139 & GLY 545, RESPECTIVELY, IS DUE TO A PCR ERROR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jgi.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jgi.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jgi_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 1jgi_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 1jgi_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1jgi_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jgi ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jgi | HTTPS FTP |
-Related 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: 71588.117 Da / Num. of mol.: 1 / Mutation: E328Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria polysaccharea (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZEU2, amylosucrase |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
#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: 2.37 Å3/Da / Density % sol: 48.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.106 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.106 Å / Relative weight: 1 |
Reflection | Resolution: 2→3 Å / Num. all: 335382 / Num. obs: 39254 / % possible obs: 84.2 % / Redundancy: 8 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8 % / Rmerge(I) obs: 0.197 / Num. unique all: 3974 / % possible all: 86.8 |
Reflection shell | *PLUS % possible obs: 86.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 953468.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.031 Å2 / ksol: 0.338146 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→27.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.214 |