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Yorodumi- PDB-8qmt: Succinic semialdehyde dehydrogenase from E. coli with Q262R subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qmt | ||||||
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Title | Succinic semialdehyde dehydrogenase from E. coli with Q262R substitution and bound NAD+, succinic semialdehyde | ||||||
Components | Succinate semialdehyde dehydrogenase [NAD(P)+] Sad | ||||||
Keywords | OXIDOREDUCTASE / succinic semialdehyde / dehydrogenase | ||||||
Function / homology | Function and homology information succinate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase [NAD(P)+] activity / putrescine catabolic process / succinate-semialdehyde dehydrogenase (NAD+) activity / cellular detoxification of nitrogen compound / gamma-aminobutyric acid catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / arginine catabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | He, H. / Zarzycki, J. / Erb, T.J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies Authors: He, H. / Gomez-Coronado, P.A. / Zarzycki, J. / Barthel, S. / Kahnt, J. / Claus, P. / Klein, M. / Klose, M. / de Crecy-Lagard, V. / Schindler, D. / Paczia, N. / Glatter, T. / Erb, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qmt.cif.gz | 714.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qmt.ent.gz | 594.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qmt_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8qmt_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8qmt_validation.xml.gz | 88.2 KB | Display | |
Data in CIF | 8qmt_validation.cif.gz | 120.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/8qmt ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qmt | HTTPS FTP |
-Related structure data
Related structure data | 8qmqC 8qmrC 8qmsC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49798.754 Da / Num. of mol.: 4 / Mutation: Q262R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: sad, yneI, b1525, JW5247 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P76149, succinate-semialdehyde dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-SSN / #4: 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: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14.8 mg/mL of SAD_Q262R in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was complemented with 5 mM NAD+. The enzyme was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, pH 7.5 , 20 % (w/v) ...Details: 14.8 mg/mL of SAD_Q262R in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was complemented with 5 mM NAD+. The enzyme was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, pH 7.5 , 20 % (w/v) PEG4000. The final drop size was 3 uL. The drop was complemented with 6 mM succininc semialdehyde and 25 % (v/v) PEG400 before flash freezing the crystals in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→29.55 Å / Num. obs: 174478 / % possible obs: 98.6 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.102 / Net I/σ(I): 16.73 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.4993 Å / Origin y: -29.453 Å / Origin z: -30.2199 Å
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Refinement TLS group | Selection details: all |