+Open data
-Basic information
Entry | Database: PDB / ID: 1brm | ||||||
---|---|---|---|---|---|---|---|
Title | ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI | ||||||
Components | ASPARTATE-SEMIALDEHYDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ESCHERICHIA COLI / ENZYME / NADP | ||||||
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 / diaminopimelate biosynthetic process / isoleucine 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 / diaminopimelate biosynthetic process / isoleucine 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 / SYNCHROTRON / SIR / Resolution: 2.5 Å | ||||||
Authors | Hadfield, A.T. / Kryger, G. / Ouyang, J. / Ringe, D. / Petsko, G.A. / Viola, R.E. | ||||||
Citation | 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. / Kryger, G. / Ouyang, J. / Petsko, G.A. / Ringe, D. / Viola, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1brm.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1brm.ent.gz | 172.7 KB | Display | PDB format |
PDBx/mmJSON format | 1brm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1brm_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1brm_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 1brm_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 1brm_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1brm ftp://data.pdbj.org/pub/pdb/validation_reports/br/1brm | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 40056.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ASD / Plasmid: PGEM / Cell line (production host): JM109 / Gene (production host): ASD / Production host: Escherichia coli (E. coli) References: UniProt: P0A9Q9, aspartate-semialdehyde dehydrogenase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0098 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0098 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 37745 / % possible obs: 79.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.49→2.59 Å / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / % possible all: 59.9 |
Reflection | *PLUS % possible obs: 86 % / Num. measured all: 116166 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 59.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR / Resolution: 2.5→28 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 33159 / Num. reflection Rfree: 3466 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.18 |