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Yorodumi- PDB-8wou: The crystal structure of aspartate aminotransferases Lpg0070 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wou | |||||||||
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Title | The crystal structure of aspartate aminotransferases Lpg0070 from Legionella pneumophila | |||||||||
Components | Aminotransferase | |||||||||
Keywords | TRANSFERASE / Aspartate aminotransferase / Legionella pneumophila | |||||||||
Function / homology | Function and homology information : / Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | Legionella pneumophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | |||||||||
Authors | Gao, Y.S. / Hua, L. / Xie, R. | |||||||||
Funding support | China, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Crystal structure of an aspartate aminotransferase Lpg0070 from Legionella pneumophila. Authors: Gao, Y. / Yang, X. / Hua, L. / Wang, M. / Ge, Q. / Wang, W. / Wang, N. / Ma, J. / Ge, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wou.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wou.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 8wou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wou_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8wou_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8wou_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 8wou_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/8wou ftp://data.pdbj.org/pub/pdb/validation_reports/wo/8wou | HTTPS FTP |
-Related structure data
Related structure data | 8wkjC 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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Unit cell |
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-Components
#1: Protein | Mass: 43822.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) Gene: C3927_15565, DIZ43_09905, ERS253283_01083, NCTC12000_00087 Production host: Escherichia coli (E. coli) References: UniProt: A0A130QXX8, Transferases; Transferring nitrogenous groups; Transaminases #2: Chemical | ChemComp-SO4 / #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: 2.89 Å3/Da / Density % sol: 57.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium sulfate 20% w/v PEG 3350 10% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2023 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→75.86 Å / Num. obs: 55245 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 45.06 Å2 / CC1/2: 0.991 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.14→2.2 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4077 / CC1/2: 0.579 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→75.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.256 / Average fsc free: 0.9137 / Average fsc work: 0.9295 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.211 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→75.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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