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Yorodumi- PDB-3pwk: Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pwk | ||||||
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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 Binding / 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: 1.5 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 | 3pwk.cif.gz | 322.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pwk.ent.gz | 258.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pwk ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pwk | HTTPS FTP |
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-Related structure data
Related structure data | 3pwsC 3pylC 3pyxC 3pzbC 3pzrC 3q0eC 3q11C 3q1lC 2gz2S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40038.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP23-BS72 / Gene: CGSSp23BS72_03388 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase |
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-Non-polymers , 5 types, 783 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 47.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% 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: 1.03 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2010 |
Radiation | Monochromator: Double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 102882 / % possible obs: 86.6 % / Redundancy: 2.8 % / Rsym value: 0.034 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.18 / % possible all: 43.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2GZ2 Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.909 / SU ML: 0.033 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.623 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.499→1.538 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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