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Yorodumi- PDB-3pzr: Crystals structure of aspartate beta-Semialdehyde dehydrogenase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pzr | ||||||
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Title | Crystals structure of aspartate beta-Semialdehyde dehydrogenase from Vibrio Cholerae with NADP and product of S-carbamoyl-L-cysteine | ||||||
Components | Aspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / isoleucine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Pavlovsky, A.G. / Potente, N. / 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 | 3pzr.cif.gz | 312.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pzr.ent.gz | 266.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pzr ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pzr | HTTPS FTP |
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-Related structure data
Related structure data | 3pwkC 3pwsC 3pylC 3pyxC 3pzbC 3q0eC 3q11C 3q1lC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40541.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_2036 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (de3) References: UniProt: Q9KQG2, aspartate-semialdehyde dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% PEG 3350, 0.1 M tris-HCL, 0.2 M Na-acetate, 10 mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 12, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→23 Å / Num. obs: 71858 / % possible obs: 84.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 6534 / Rsym value: 0.35 / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.907 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R Free: 0.123 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.127 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 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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