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Yorodumi- PDB-8ixi: Crystal structure of aldehyde dehydrogenase (EC 1.2.1.3) Klebsiel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ixi | ||||||
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Title | Crystal structure of aldehyde dehydrogenase (EC 1.2.1.3) Klebsiella pneumoniae | ||||||
Components | Aldehyde dehydrogenase protein | ||||||
Keywords | OXIDOREDUCTASE / aldehyde dehydrogenase | ||||||
Function / homology | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / aldehyde dehydrogenase (NAD+) activity / transferase activity / Protein kinase-like domain superfamily / Aldehyde dehydrogenase protein Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Zhang, Z.L. / Gao, C. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Systems engineering of Escherichia coli for high-level glutarate production from glucose. Authors: Zhang, Z. / Chu, R. / Wei, W. / Song, W. / Ye, C. / Chen, X. / Wu, J. / Liu, L. / Gao, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ixi.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ixi.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ixi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixi ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixi | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33849.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mph2, mph(E), mphE, IE995_27805, NCTC13443_00027 / Production host: Escherichia coli (E. coli) / References: UniProt: D8L2F8, aldehyde dehydrogenase (NAD+) #2: 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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Agnesium chloride hexahydrate, Bis-tris pH 6.5, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Dec 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→45.78 Å / Num. obs: 28209 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.081 / Rrim(I) all: 0.169 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.28→2.36 Å / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2776 / CC1/2: 0.604 / Rpim(I) all: 0.041 / Rrim(I) all: 0.088 |
-Processing
Software | Name: XDS / Classification: data scaling | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→45.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.253 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.549 Å2
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Refinement step | Cycle: 1 / Resolution: 2.28→45.78 Å
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Refine LS restraints |
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