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Yorodumi- PDB-1pu2: Crystal Structure of the K246R Mutant of Aspartate Semialdehyde D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pu2 | ||||||
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Title | Crystal Structure of the K246R Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae | ||||||
Components | Aspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / aspartate semialdehyde dehydrogenase / phosphate / enzyme | ||||||
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: 2.06 Å | ||||||
Authors | Blanco, J. / Moore, R.A. / Faehnle, C.R. / Coe, D.M. / Viola, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: The role of substrate-binding groups in the mechanism of aspartate-beta-semialdehyde dehydrogenase. Authors: Blanco, J. / Moore, R.A. / Faehnle, C.R. / Coe, D.M. / 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 | 1pu2.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pu2.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pu2 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pu2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ozaC 1pqpC 1pquC 1pr3C 1ps8C 1q2xC 1nwcS 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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-Components
#1: Protein | Mass: 40728.852 Da / Num. of mol.: 1 / Mutation: K246R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: asd / Plasmid: pET41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P44801, aspartate-semialdehyde dehydrogenase |
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#2: 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: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% PEG 3350, 0.2M ammonium acetate, 0.1 Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 18, 2002 |
Radiation | Monochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 27766 / Num. obs: 27081 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.055 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.86→1.94 Å / Mean I/σ(I) obs: 4.8 / Num. unique all: 1025 / Rsym value: 0.301 / % possible all: 30.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWC Resolution: 2.06→40.33 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.5384 Å2 / ksol: 0.346628 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→40.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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