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- PDB-1nwh: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Ha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nwh | ||||||
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Title | Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae as a Tetrahedral Hemithioacetal Reaction Intermediate at 2.0 A | ||||||
![]() | Aspartate-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / aspartate semialdehyde dehydrogenase / aspartate semialdehyde / Haemophilus influenzae / tetrahedral intermediate / hemithioacetal | ||||||
Function / homology | ![]() aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blanco, J. / Moore, R.A. / Viola, R.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153 KB | Display | ![]() |
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PDB format | ![]() | 121 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nwcSC ![]() 1nx6C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a homodimer |
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Components
#1: Protein | Mass: 40700.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P44801, aspartate-semialdehyde dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 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 273K | ||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001 |
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→99 Å / Num. all: 40026 / Num. obs: 39040 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.83 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3591 / % possible all: 76.7 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 83.9 % / Num. measured all: 150757 |
Reflection shell | *PLUS % possible obs: 76.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NWC Resolution: 2→29.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 502711.59 / Data cutoff high rms absF: 502711.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.4439 Å2 / ksol: 0.353521 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / 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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