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Yorodumi- PDB-5ykt: Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ykt | ||||||
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Title | Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286A) from Pseudomonas aeruginosa PAO1 in complex with PMP | ||||||
Components | Probable aminotransferase | ||||||
Keywords | TRANSFERASE / glutamate-1-semialdehyde-aminomutase / C5 pathway | ||||||
Function / homology | Function and homology information glutamate-1-semialdehyde 2,1-aminomutase activity / organonitrogen compound metabolic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Li, S. / Zhang, Q. / Bartlam, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of a glutamate-1-semialdehyde-aminomutase from Pseudomonas aeruginosa PAO1. Authors: Li, S. / Lou, X. / Xu, Y. / Teng, X. / Che, S. / Liu, R. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ykt.cif.gz | 371.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ykt.ent.gz | 300.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ykt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5ykt ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5ykt | HTTPS FTP |
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-Related structure data
Related structure data | 5ykrSC 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 5 - 457 / Label seq-ID: 5 - 457
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-Components
#1: Protein | Mass: 51028.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4088 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9HWU0, glutamate-1-semialdehyde 2,1-aminomutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Tris pH 6.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 121760 / % possible obs: 99.6 % / Redundancy: 6.5 % / Net I/σ(I): 32.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YKR Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.896 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.237 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→50 Å
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Refine LS restraints |
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