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Yorodumi- PDB-1zs2: Amylosucrase Mutant E328Q in a ternary complex with sucrose and m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zs2 | |||||||||
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Title | Amylosucrase Mutant E328Q in a ternary complex with sucrose and maltoheptaose | |||||||||
Components | amylosucrase | |||||||||
Keywords | TRANSFERASE / ternary complex / (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: 2.16 Å | |||||||||
Authors | Skov, L.K. / Mirza, O. / Sprogoe, D. / van der Veen, B.A. / Remaud-Simeon, M. / Albenne, C. / Monsan, P. / Gajhede, M. | |||||||||
Citation | Journal: BIOCATAL.BIOTRANSFOR. / Year: 2006 Title: Crystal structure of the Glu328Gln mutant of Neisseria polysaccharea amylosucrase in complex with sucrose and maltoheptaose Authors: Skov, L.K. / Mirza, O. / Sprogoe, D. / van der Veen, B.A. / Remaud-Simeon, M. / Albenne, C. / Monsan, P. / Gajhede, M. #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 and the active site mutant glu328gln in complex with the natural substrate sucrose Authors: Mirza, O. / Skov, L.K. / Remaud-Simeon, M. / De Montalk, G.P. / Albenne, C. / Monsan, P. / Gajhede, M. #3: Journal: J.Biol.Chem. / Year: 2002 Title: Oligosaccharide and sucrose complexes of amylosucrase Authors: Skov, L.K. / Mirza, O. / Sprogoe, D. / Dar, I. / Remaud-Simeon, M. / Albenne, C. / Monsan, P. / Gajhede, M. | |||||||||
History |
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Remark 999 | SEQUENCE THE DISCREPANCY BETWEEN RESIDUES TYR 131 AND THE GENBANK SEQUENCE DATABASE REFERENCE, ...SEQUENCE THE DISCREPANCY BETWEEN RESIDUES TYR 131 AND THE GENBANK SEQUENCE DATABASE REFERENCE, ACCESSION 4107260, RESIDUES 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 | 1zs2.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zs2.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/1zs2 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/1zs2 | HTTPS FTP |
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-Related structure data
Related structure data | 1g5aS 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 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: GenBank: 4107260, UniProt: Q9ZEU2*PLUS, amylosucrase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
#5: 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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, SODIUM CHLORIDE, TRIS-HCL, EDTA, HEPES, DTT, sucrose, maltoheptaose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.983 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 2000 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→30 Å / Num. all: 37637 / Num. obs: 37336 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.16→2.24 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.3 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1g5a Resolution: 2.16→28.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 424875.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3346 Å2 / ksol: 0.306013 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.16→28.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.3 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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