+Open data
-Basic information
Entry | Database: PDB / ID: 2zy3 | ||||||
---|---|---|---|---|---|---|---|
Title | dodecameric L-aspartate beta-decarboxylase | ||||||
Components | L-aspartate beta-decarboxylase | ||||||
Keywords | LYASE / pyridoxal 5'-phosphate / aminotransferase | ||||||
Function / homology | Function and homology information aspartate 4-decarboxylase / aspartate 4-decarboxylase activity / 1-aminocyclopropane-1-carboxylate synthase activity / alanine biosynthetic process / aspartate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis subsp. faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chen, H.-J. / Ko, T.-P. / Lee, C.-Y. / Wang, N.-C. / Wang, A.H.-J. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate beta-Decarboxylase Authors: Chen, H.-J. / Ko, T.-P. / Lee, C.-Y. / Wang, N.-C. / Wang, A.H.-J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zy3.cif.gz | 645 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zy3.ent.gz | 530.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zy3_validation.pdf.gz | 519.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zy3_full_validation.pdf.gz | 597.9 KB | Display | |
Data in XML | 2zy3_validation.xml.gz | 139.2 KB | Display | |
Data in CIF | 2zy3_validation.cif.gz | 198.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/2zy3 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/2zy3 | HTTPS FTP |
-Related structure data
Related structure data | 2zy2SC 2zy4C 2zy5C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 61173.480 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis subsp. faecalis (bacteria) Strain: subsp. faecalis / Gene: asdA-AF / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93QX0, aspartate 4-decarboxylase #2: Chemical | ChemComp-PLP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.53 % |
---|---|
Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 7.4 Details: 0.1M Tris-HCl (pH 7.4), 0.1M Lithium sulfate, 15% PEG 4000, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 116669 / Num. obs: 115036 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / Num. unique all: 11108 / % possible all: 96.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZY2 Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Bsol: 44.429 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 121.29 Å2 / Biso mean: 38.795 Å2 / Biso min: 5.81 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.076
|