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- PDB-4ogd: Crystal structure of succinic semialdehyde dehydrogenase from Str... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ogd | ||||||
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Title | Crystal structure of succinic semialdehyde dehydrogenase from Streptococcus pyogenes in complex with NADP+ as the cofactor | ||||||
![]() | Succinate-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / SSADH / GabD / Rossmann Fold / Dehydrogenase / NADP Binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jang, E.H. / Park, S.A. / Chi, Y.M. / Lee, K.S. | ||||||
![]() | ![]() Title: Kinetic and Structural Characterization for Cofactor Preference of 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.4 KB | Display | ![]() |
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PDB format | ![]() | 153.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ohtC ![]() 3jz4S 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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Details | The biological assembly is a dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 51861.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: bacteria Source: (gene. exp.) ![]() Strain: Streptococcus pyogenes / Gene: gabD, MGAS1882_0809 / Plasmid: pET-28a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES monohydrate and 18-23% (w/v) PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 1262499 / Num. obs: 128443 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 12.14 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.058 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5681 / Rsym value: 0.352 / % possible all: 88.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3JZ4 Resolution: 1.6→17.97 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 17.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→17.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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