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Yorodumi- PDB-1zja: Crystal structure of the trehalulose synthase MutB from Pseudomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zja | ||||||
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Title | Crystal structure of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45 (triclinic form) | ||||||
Components | Trehalulose synthase | ||||||
Keywords | ISOMERASE / trehalulose synthase / sucrose isomerase / alpha-amylase family / (beta/alpha)8 barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas mesoacidophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ravaud, S. / Robert, X. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization. Authors: Ravaud, S. / Robert, X. / Watzlawick, H. / Haser, R. / Mattes, R. / Aghajari, N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45. Authors: Ravaud, S. / Watzlawick, H. / Haser, R. / Mattes, R. / Aghajari, N. | ||||||
History |
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Remark 999 | SEQUENCE According to authors, there is no database reference for the protein sequence as it is ... SEQUENCE According to authors, there is no database reference for the protein sequence as it is patented (U.S. Patent *5786140*). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zja.cif.gz | 273.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zja.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zja ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zja | HTTPS FTP |
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-Related structure data
Related structure data | 2pwdC 2pweC 2pwfC 2pwgC 2pwhC 1m53S 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
#1: Protein | Mass: 63938.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Strain: MX-45 / Plasmid: pJOE2702 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, isomaltulose synthase #2: Chemical | #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 20000, Tris-HCl, L-cysteine, pH 8.5, temperature 290K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2004 |
Radiation | Monochromator: synchrotron optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39 Å / Num. all: 156700 / Num. obs: 156700 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.086 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.277 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M53 Resolution: 1.6→39 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 930872.34 / 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: 47.7909 Å2 / ksol: 0.367044 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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