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Yorodumi- PDB-3pws: Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pws | ||||||
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Title | Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus pneumoniae with 2',5'-Adenosine diphosphate and D-2-aminoadipate | ||||||
Components | Aspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Dehydrogenase / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Pavlovsky, A.G. / Viola, R.E. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2012 Title: Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family. Authors: Pavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pws.cif.gz | 144.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pws.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 3pws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pws ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pws | HTTPS FTP |
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-Related structure data
Related structure data | 3pwkC 3pylC 3pyxC 3pzbC 3pzrC 3q0eC 3q11C 3q1lC 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: 40038.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: CGSSp23BS72_03388 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: 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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.1M MES, 0.1 M ammonium acetate, 10 mM DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2009 Details: Horizontally and vertically focusing bimorph mirrors in Kirkpatrick-Baez config uration |
Radiation | Monochromator: Double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.73 Å / Num. obs: 40802 / % possible obs: 82 % / Redundancy: 2.1 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.062 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 3233 / Rsym value: 0.125 / % possible all: 64.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→36.73 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.042 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 19.779 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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