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Yorodumi- PDB-4ywv: Structural insight into the substrate inhibition mechanism of NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ywv | ||||||
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Title | Structural insight into the substrate inhibition mechanism of NADP+-dependent succinic semialdehyde dehydrogenase from Streptococcus pyogenes | ||||||
Components | Succinic semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Succinic semialdehyde dehydrogenase / Streptococcus pyogenes / Substrate inhibition / ESS-complex structure | ||||||
Function / homology | Function and homology information succinate-semialdehyde dehydrogenase (NADP+) / succinate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase [NAD(P)+] activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes MGAS1882 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Park, S.A. / Jang, E.H. / Chi, Y.M. / Lee, K.S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Structural insight into the substrate inhibition mechanism of NADP(+)-dependent succinic semialdehyde dehydrogenase from Streptococcus pyogenes. Authors: Jang, E.H. / Park, S.A. / Chi, Y.M. / Lee, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ywv.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ywv.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ywv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ywv_validation.pdf.gz | 460.8 KB | Display | wwPDB validaton report |
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Full document | 4ywv_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 4ywv_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 4ywv_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywv ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywv | HTTPS FTP |
-Related structure data
Related structure data | 4ywuC 4ohtS 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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-Components
#1: Protein | Mass: 51861.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes MGAS1882 (bacteria) Strain: MGAS1882 / Gene: gabD / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0J9X1M8*PLUS, succinate-semialdehyde dehydrogenase (NADP+) #2: Chemical | ChemComp-SSN / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS BASED ON GENBANK AFC68023 | |
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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: 3.82 Å3/Da / Density % sol: 67.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Sodium acetate trihydrate pH 4.6, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 56597 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.1 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OHT Resolution: 2.4→41.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 57903.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.7143 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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