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Yorodumi- PDB-2r00: crystal structure of aspartate semialdehyde dehydrogenase II comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r00 | ||||||
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Title | crystal structure of aspartate semialdehyde dehydrogenase II complexed with ASA from vibrio cholerae | ||||||
Components | (Aspartate-semialdehyde dehydrogenase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / aspartate semialdehyde dehydrogenase / conformational change / half-of-sites-reactivity / protein evolution / sequence homology / subunit communication / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / NADP | ||||||
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 | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Viola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae. Authors: Viola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r00.cif.gz | 206.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r00.ent.gz | 163.1 KB | Display | PDB format |
PDBx/mmJSON format | 2r00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r00 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r00 | HTTPS FTP |
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-Related structure data
Related structure data | 2qz9C 1ys4S C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37277.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: E1 Tor / Gene: asd / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P23247, aspartate-semialdehyde dehydrogenase #2: Protein | | Mass: 37394.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: E1 Tor / Gene: asd / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P23247, aspartate-semialdehyde dehydrogenase #3: Chemical | ChemComp-OEG / | #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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M sodium citrate pH 5.5, 27% PEG8000, 0.3M ammonium acetate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 73968 / Num. obs: 70525 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rsym value: 0.053 / Net I/σ(I): 27 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.33 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YS4 Resolution: 2.03→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.746 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.037 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.026→2.078 Å / Total num. of bins used: 20
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