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Yorodumi- PDB-1gl3: ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE IN COMPLEX WITH NADP AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gl3 | ||||||
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Title | ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE IN COMPLEX WITH NADP AND SUBSTRATE ANALOGUE S-METHYL CYSTEINE SULFOXIDE | ||||||
Components | ASPARTATE-SEMIALDEHYDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ESCHERICHIA COLI / ENZYME / NADP / DIAMINOPIMELATE BIOSYNTHESI LYSINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information homoserine biosynthetic process / 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 ...homoserine biosynthetic process / 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 / DNA damage response / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hadfield, A.T. / Kryger, G. / Ouyang, J. / Ringe, D. / Petsko, G.A. / Viola, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Active Site Analysis of the Potential Antimicrobial Target Aspartate Semialdehyde Dehydrogenase. Authors: Hadfield, A.T. / Shammas, C. / Kryger, G. / Ringe, D. / Petsko, G.A. / Ouyang, J. / Viola, R.E. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Structure of Aspartate-Beta-Semialdehyde Dehydrogenase from Escherichia Coli, a Key Enzyme in the Aspartate Family of Amino Acid Biosynthesis Authors: Hadfield, A.T. / Kryger, G. / Ouyang, J. / Petsko, G.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 | 1gl3.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gl3.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 1gl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/1gl3 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/1gl3 | HTTPS FTP |
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-Related structure data
Related structure data | 1brmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9746, 0.224, -0.0013), Vector: |
-Components
#1: Protein | Mass: 40056.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cell line: JM109 / Plasmid: PGEM / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): JM109 References: UniProt: P00353, UniProt: P0A9Q9*PLUS, aspartate-semialdehyde dehydrogenase #2: Chemical | ChemComp-CYS / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: RESERVOIR: 19% PEG 4K, 0.35M MGCL2, 0.2 M NH4AC 0.1M TRIS, pH 4.60 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1996 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→28 Å / Num. obs: 41666 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.103 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 1.5 / % possible all: 61.6 |
Reflection | *PLUS Num. obs: 22099 / Num. measured all: 41666 |
Reflection shell | *PLUS % possible obs: 61.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BRM Resolution: 2.6→28 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.74 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.3 Å2 |