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- PDB-8xhd: Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xhd | ||||||
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Title | Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor and L-glutamate | ||||||
![]() | 8-amino-7-oxononanoate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, M.J. / Zhang, D.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.3 KB | Display | ![]() |
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PDB format | ![]() | 126 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8i7uC ![]() 8xhaSC ![]() 8xhkC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 42929.961 Da / Num. of mol.: 2 / Mutation: S87G Source method: isolated from a genetically manipulated source Details: The sequence of organism Streptomyces albogriseolus 1-36 is not available, replaced by A0A6B9KSL0 temporarily. Source: (gene. exp.) ![]() Gene: alb29 / Production host: ![]() ![]() ![]() References: UniProt: A0A6B9KSL0, ![]() #2: Chemical | ChemComp-PGU / | #3: Chemical | ChemComp-PLP / | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.45 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: liquid diffusion Details: 0.1 M Amino acid mix, 0.1 M Buffer system 3, pH8.5, 30% v/v Precipitant Mix2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→101.96 Å / Num. obs: 32498 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Rrim(I) all: 0.113 / Χ2: 1.14 / Net I/σ(I): 20.3 / Num. measured all: 368062 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.274 / Num. unique obs: 3210 / CC1/2: 0.712 / CC star: 0.912 / Rpim(I) all: 0.389 / Rrim(I) all: 1.306 / Χ2: 0.95 / % possible all: 99.97 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 8XHA Resolution: 2.7→43.68 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26 / 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: 2.7→43.68 Å
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Refine LS restraints |
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LS refinement shell |
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