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Yorodumi- PDB-8cek: Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cek | ||||||
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Title | Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with NADPH | ||||||
Components | Succinate-semialdehyde dehydrogenase (acetylating) | ||||||
Keywords | OXIDOREDUCTASE / SSA / succinic semialdehyde / NADPH / NADP+ / SucD / ssr / succinyl-CoA / mesaconyl-CoA / mesaconyl-C1-CoA / SucD_Ck / CkSucD | ||||||
Function / homology | succinate-semialdehyde dehydrogenase (acylating) / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Succinate-semialdehyde dehydrogenase (acetylating) Function and homology information | ||||||
Biological species | Clostridium kluyveri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Pfister, P. / Diehl, C. / Erb, T.J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis. Authors: Pfister, P. / Diehl, C. / Hammarlund, E. / Carrillo, M. / 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 | 8cek.cif.gz | 707.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cek.ent.gz | 591.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cek_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8cek_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8cek_validation.xml.gz | 74.6 KB | Display | |
Data in CIF | 8cek_validation.cif.gz | 104.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8cek ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8cek | HTTPS FTP |
-Related structure data
Related structure data | 8ceiC 8cejC 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49029.910 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium kluyveri (bacteria) / Gene: sucD, CKL_3015 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P38947, succinate-semialdehyde dehydrogenase (acylating) #2: Chemical | ChemComp-NAP / #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: 3.23 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 45 % w/v Pentaerythritol Propoxylate (5/4 PO/OH) 100 mM MES; pH 6.5 400 mM Potassium chloride PH range: 6.5-7.8 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→39.44 Å / Num. obs: 159239 / % possible obs: 98.6 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rpim(I) all: 0.059 / Rrim(I) all: 0.215 / Net I/σ(I): 8.5 / Num. measured all: 2045343 |
Reflection shell | Resolution: 2.04→2.15 Å / % possible obs: 90.4 % / Redundancy: 8 % / Num. measured all: 169254 / Num. unique obs: 21156 / CC1/2: 0.329 / Rpim(I) all: 0.966 / Rrim(I) all: 2.931 / Net I/σ(I) obs: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.84 / 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: 2.15→29.66 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: 14.3316 Å / Origin y: -23.6325 Å / Origin z: 47.3039 Å
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Refinement TLS group | Selection details: all |