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Yorodumi- PDB-2jf4: Family 37 trehalase from Escherichia coli in complex with validox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jf4 | ||||||
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Title | Family 37 trehalase from Escherichia coli in complex with validoxylamine | ||||||
Components | PERIPLASMIC TREHALASE | ||||||
Keywords | HYDROLASE / FAMILY 37 / INHIBITOR / TREHALASE / GLYCOSIDE HYDROLASE / PERIPLASMIC / GLYCOSIDASE / VALIDOXYLAMINE | ||||||
Function / homology | Function and homology information alpha,alpha-trehalase / trehalose catabolic process / alpha,alpha-trehalase activity / cellular hyperosmotic response / outer membrane-bounded periplasmic space / DNA damage response Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Gibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: Molecular Basis for Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors. Authors: Gibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jf4.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jf4.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 2jf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jf4_validation.pdf.gz | 799.6 KB | Display | wwPDB validaton report |
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Full document | 2jf4_full_validation.pdf.gz | 803.1 KB | Display | |
Data in XML | 2jf4_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2jf4_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jf4 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jf4 | 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: 61183.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-565 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13482, alpha,alpha-trehalase |
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#2: Chemical | ChemComp-VDM / ( |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE CLEAVED DURING ...THE FIRST 30 RESIDUES CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | pH: 6.5 Details: 15 MG/ML PROTEIN. 25% PEG3350 AND 0.1 M BIS-TRIS HCL, PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97931 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 27378 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.2→28.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.672 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY CAN BE OBSERVED FOR THE CHAIN BETWEEN 101 AND 113.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→28.57 Å
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Refine LS restraints |
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