+Open data
-Basic information
Entry | Database: PDB / ID: 8iyf | ||||||
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Title | Structure of VldE-H182A in complex with GDP | ||||||
Components | Validamine 7-phosphate valienyltransferase | ||||||
Keywords | TRANSFERASE / Pseudoglycosyltransferase / validamine | ||||||
Function / homology | Function and homology information validamine 7-phosphate valienyltransferase / trehalose metabolism in response to stress / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / hexosyltransferase activity / antibiotic biosynthetic process / cellular response to heat / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces hygroscopicus subsp. limoneus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wong, C.P. / Mori, T. / Mahmud, T. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of VldE-H182A in complex with GDP Authors: Wong, C.P. / Mori, T. / Mahmud, T. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyf.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyf.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 8iyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyf ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyf | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54939.465 Da / Num. of mol.: 2 / Mutation: H182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus subsp. limoneus (bacteria) Gene: vldE, SHL15_8006 / Production host: Escherichia coli (E. coli) References: UniProt: Q15JG1, validamine 7-phosphate valienyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl, pH8.5, 26% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.01 Å / Num. obs: 74391 / % possible obs: 97.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4500 / CC1/2: 0.805 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.01 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.4978 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.01 Å
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Refine LS restraints |
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LS refinement shell |
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