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Yorodumi- PDB-1nx6: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Ha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nx6 | ||||||
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Title | Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae as a Tetrahedral Hemithiocetal Reaction intermediate with Phosphate at 2.15 A | ||||||
Components | Aspartate-Semialdehyde Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / aspartate-semialdehyde dehydrogenase / aspartate semialdehyde / Haemophilus influenzae / tetrahedal intermediate / hemithiocetal / phosphate | ||||||
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 | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Blanco, J. / Moore, R.A. / Viola, R.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Capture of an Intermediate in the Catalytic Cycle of L-Aspartate-beta-Semialdehyde Dehydrogenase Authors: Blanco, J. / Moore, R.A. / 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 | 1nx6.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nx6.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nx6 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nx6 | HTTPS FTP |
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-Related structure data
Related structure data | 1nwcC 1nwhSC 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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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 40700.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: asd / Plasmid: PET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P44801, aspartate-semialdehyde dehydrogenase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-24% PEG 3350, 0.2 M Ammonium Acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100 Å / Num. all: 20308 / Num. obs: 19724 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.06 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1992 / % possible all: 99.9 |
Reflection | *PLUS % possible obs: 99.9 % / Num. measured all: 143627 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NWH Resolution: 2.15→40.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 280448.71 / Data cutoff high rms absF: 280448.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.3946 Å2 / ksol: 0.312921 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→40.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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