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Yorodumi- PDB-7v58: Structural insights into the substrate selectivity of acyl-CoA tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v58 | ||||||
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Title | Structural insights into the substrate selectivity of acyl-CoA transferase | ||||||
Components | 2-amino-3-ketobutyrate coenzyme A ligase | ||||||
Keywords | TRANSFERASE / acyltransferase / pyridoxal phosphate / sphingolipids | ||||||
Function / homology | Function and homology information glycine C-acetyltransferase / glycine C-acetyltransferase activity / L-threonine catabolic process to glycine / biosynthetic process / ligase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Vibrio proteolyticus NBRC 13287 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Chang, H.Y. / Ko, T.P. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Colloids Surf B Biointerfaces / Year: 2022 Title: Structural insights into the substrate selectivity of alpha-oxoamine synthases from marine Vibrio sp. QWI-06. Authors: Chang, H.Y. / Lo, L.H. / Lan, Y.H. / Hong, M.X. / Chan, Y.T. / Ko, T.P. / Huang, Y.R. / Cheng, T.H. / Liaw, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v58.cif.gz | 226.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v58.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 7v58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v58_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7v58_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7v58_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 7v58_validation.cif.gz | 59.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/7v58 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v58 | HTTPS FTP |
-Related structure data
Related structure data | 7v5iC 1fc4S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43729.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio proteolyticus NBRC 13287 (bacteria) Gene: kbl, VPR01S_15_00210 / Production host: Escherichia coli (E. coli) / References: UniProt: U3BPN5, glycine C-acetyltransferase |
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-Non-polymers , 5 types, 808 molecules
#2: Chemical | ChemComp-PLP / | ||||||
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#3: Chemical | ChemComp-MES / #4: Chemical | #5: Chemical | ChemComp-GLY / | #6: Water | ChemComp-HOH / | |
-Details
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: 3 Å3/Da / Density % sol: 59.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate, pH 6.5, 0.2 M Lithium sulfate, 1 mM L-glycine, 30% polyethylene glycol (PEG) 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 90896 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 19.97 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.84→1.91 Å / Rmerge(I) obs: 0.729 / Num. unique obs: 9025 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fc4 Resolution: 1.84→25.54 Å / SU ML: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.254 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: 25.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→25.54 Å
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Refine LS restraints |
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LS refinement shell |
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