[English] 日本語
Yorodumi- PDB-1pqp: Crystal Structure of the C136S Mutant of Aspartate Semialdehyde D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pqp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the C136S Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae Bound with Aspartate Semialdehyde and Phosphate | |||||||||
Components | Aspartate-semialdehyde dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Enzyme / L-aspartate semialdehyde / L-aspartate semialdehyde dehydrogenase / phosphate | |||||||||
Function / homology | Function and homology information 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 | Haemophilus influenzae Rd (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||
Authors | Blanco, J. / Moore, R.A. / Faehnle, C.R. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pqp.cif.gz | 87 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pqp.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pqp_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1pqp_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 1pqp_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1pqp_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqp ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqp | HTTPS FTP |
-Related structure data
Related structure data | 1ozaC 1pquC 1pr3C 1ps8C 1pu2C 1q2xC 1nwcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 40567.672 Da / Num. of mol.: 1 / Mutation: C136S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: asd / Plasmid: PET43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P44801, aspartate-semialdehyde dehydrogenase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-HSE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% PEG 3350, 0.2M Ammonium acetate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
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: 1.91→50 Å / Num. all: 27514 / Num. obs: 27474 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 10.9 Å2 / Rsym value: 0.049 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.91→1.98 Å / Mean I/σ(I) obs: 13.4 / Num. unique all: 2447 / Rsym value: 0.118 / % possible all: 85.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWC Resolution: 2.06→37.64 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
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.9707 Å2 / ksol: 0.371209 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→37.64 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|