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- PDB-5ykr: Crystal structure of a glutamate-1-semialdehyde-aminomutase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ykr | ||||||
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Title | Crystal structure of a glutamate-1-semialdehyde-aminomutase from Pseudomonas aeruginosa PAO1 | ||||||
![]() | Probable aminotransferase | ||||||
![]() | TRANSFERASE / glutamate-1-semialdehyde-aminomutase / C5 pathway | ||||||
Function / homology | ![]() : / glutamate-1-semialdehyde 2,1-aminomutase activity / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, S. / Zhang, Q. / Bartlam, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 399.3 KB | Display | ![]() |
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PDB format | ![]() | 324.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yktC ![]() 3bs8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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: _ / Auth seq-ID: 5 - 457 / Label seq-ID: 5 - 457
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Components
#1: Protein | Mass: 51315.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4088 / Production host: ![]() ![]() References: UniProt: Q9HWU0, glutamate-1-semialdehyde 2,1-aminomutase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 155189 / % possible obs: 100 % / Redundancy: 6.6 % / Net I/σ(I): 23.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BS8 Resolution: 1.44→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.09 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.046 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→50 Å
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Refine LS restraints |
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