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Yorodumi- PDB-5z6h: Structure of periplasmic trehalase from Diamondback moth gut bact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z6h | ||||||
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Title | Structure of periplasmic trehalase from Diamondback moth gut bacteria in the apo form | ||||||
Components | Periplasmic trehalase | ||||||
Keywords | HYDROLASE / Trehalase from insect gut bacterium / apo structure | ||||||
Function / homology | Function and homology information alpha,alpha-trehalase / trehalose catabolic process / alpha,alpha-trehalase activity / cellular hyperosmotic response / periplasmic space Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Harne, S.R. / Adhav, A.S. / Joshi, R.S. / Gayathri, P. | ||||||
Funding support | India, 1items
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Citation | Journal: Febs J. / Year: 2019 Title: Mechanistic insights into enzymatic catalysis by trehalase from the insect gut endosymbiont Enterobacter cloacae. Authors: Adhav, A. / Harne, S. / Bhide, A. / Giri, A. / Gayathri, P. / Joshi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z6h.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z6h.ent.gz | 182.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z6h_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 5z6h_full_validation.pdf.gz | 482.7 KB | Display | |
Data in XML | 5z6h_validation.xml.gz | 44 KB | Display | |
Data in CIF | 5z6h_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z6h ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z6h | HTTPS FTP |
-Related structure data
Related structure data | 5z66C 2jg0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63167.527 Da / Num. of mol.: 2 / Mutation: S32N, A35T, A553V Source method: isolated from a genetically manipulated source Details: cDNA extracted from larvae of Diamond black moth / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: treA, SAMEA2273171_02252 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR DE3 / References: UniProt: A0A156C5X3, alpha,alpha-trehalase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | The authors state that the difference with the sequence database might arise from the natural ...The authors state that the difference with the sequence database might arise from the natural variation in the population or errors in genome sequences. | |
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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: 2.12 Å3/Da / Density % sol: 42.07 % / Description: Plate-like |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.5M Ammonium sulphate, 25% PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97937 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.32 Å / Num. obs: 48818 / % possible obs: 97.9 % / Redundancy: 4.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.086 / Rrim(I) all: 0.139 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4363 / CC1/2: 0.685 / Rpim(I) all: 0.421 / Rrim(I) all: 0.678 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JG0 Resolution: 2.3→33.319 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.319 Å
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Refine LS restraints |
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LS refinement shell |
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