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Yorodumi- PDB-4zic: Crystal Structure of Aspartate Semialdehyde Dehydrogenase with NA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zic | ||||||
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Title | Crystal Structure of Aspartate Semialdehyde Dehydrogenase with NADP from Trichophyton rubrum | ||||||
Components | Aspartate Semialdehyde DehydrogenaseAspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Aspartate-semialdehyde dehydrogenase / tetramer / Complex | ||||||
Function / homology | Function and homology information aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity Similarity search - Function | ||||||
Biological species | Trichophyton rubrum BMU01672 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å | ||||||
Authors | Li, Q. / Cui, S. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural Insights into the Tetrameric State of Aspartate-beta-semialdehyde Dehydrogenases from Fungal Species Authors: Li, Q. / Mu, Z. / Zhao, R. / Dahal, G. / Viola, R.E. / Liu, T. / Jin, Q. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zic.cif.gz | 747.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zic.ent.gz | 628.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/4zic ftp://data.pdbj.org/pub/pdb/validation_reports/zi/4zic | HTTPS FTP |
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-Related structure data
Related structure data | 4zhsSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40686.613 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichophyton rubrum BMU01672 (fungus) / Strain: BMU01672 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta References: UniProt: A0A140UHG6*PLUS, aspartate-semialdehyde dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.15M Ammonium Sulfate, 0.1M Sodium Citrate, 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97876 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014 |
Radiation | Monochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97876 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 169359 / Num. obs: 168846 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.84 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 2.55→2.71 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.37 / % possible all: 99.4 |
-Processing
Software | Name: PHENIX / Version: 1.7.3_928 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZHS Resolution: 2.553→46.133 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.16 / Stereochemistry target values: ML Details: DURING DATA COLLECTION, F+ AND F- WERE CONSIDERED AS DIFFERENT REFLECTION BECAUSE THE FRIEDEL'S LAW WAS FALSE. AFTER MOLECULAR REPLACEMENT FOR STRUCTURE DETERMINATION, IN THE REFINEMENT F+ ...Details: DURING DATA COLLECTION, F+ AND F- WERE CONSIDERED AS DIFFERENT REFLECTION BECAUSE THE FRIEDEL'S LAW WAS FALSE. AFTER MOLECULAR REPLACEMENT FOR STRUCTURE DETERMINATION, IN THE REFINEMENT F+ AND F- WERE MERGED THEREFORE THE REFLECTION COUNTED WERE AROUND 50% OF DATA COLLECTION.
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.802 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.553→46.133 Å
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Refine LS restraints |
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LS refinement shell |
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