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Yorodumi- PDB-8xhk: Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xhk | ||||||
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Title | Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor | ||||||
Components | Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme | ||||||
Keywords | TRANSFERASE / complex / PLP / Dimer / alpha-Oxoamine Synthase | ||||||
Function / homology | Function and homology information 8-amino-7-oxononanoate synthase / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Streptomyces albogriseolus 1-36 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Xu, M.J. / Zhang, D.K. | ||||||
Funding support | China, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Structural and mechanistic investigations on CC bond forming alpha-oxoamine synthase allowing L-glutamate as substrate. Authors: Zhang, D.K. / Song, K.Y. / Yan, Y.Q. / Zheng, J.T. / Xu, J. / Da, L.T. / Xu, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xhk.cif.gz | 544.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xhk.ent.gz | 362.6 KB | Display | PDB format |
PDBx/mmJSON format | 8xhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/8xhk ftp://data.pdbj.org/pub/pdb/validation_reports/xh/8xhk | HTTPS FTP |
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-Related structure data
Related structure data | 8i7uSC 8xhaC 8xhdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42888.883 Da / Num. of mol.: 6 / Mutation: S87G Source method: isolated from a genetically manipulated source Details: GenBank ID is QHB15350.1 Source: (gene. exp.) Streptomyces albogriseolus 1-36 (bacteria) Gene: alb29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6B9KSL0 #2: Chemical | #3: Chemical | #4: 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: 2.48 Å3/Da / Density % sol: 50.36 % |
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Crystal grow | Temperature: 293.15 K / Method: liquid diffusion Details: 0.03M MgCl2, 0.03M CaCl2, 0.1M MES-Imidazole, pH 6.5, 20% Glycerol, 10%(w/v)PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 62296 / % possible obs: 99.51 % / Redundancy: 11.8 % / Biso Wilson estimate: 66.41 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.09468 / Rpim(I) all: 0.02891 / Rrim(I) all: 0.09909 / Net I/σ(I): 18.78 |
Reflection shell | Resolution: 2.79→2.89 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.9972 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 6367 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.2993 / % possible all: 99.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8I7U Resolution: 2.79→25.19 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1778 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: 69.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→25.19 Å
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Refine LS restraints |
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LS refinement shell |
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