[English] 日本語
Yorodumi- PDB-4dza: Crystal structure of a lysine racemase within internal aldimine l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dza | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a lysine racemase within internal aldimine linkage | ||||||
Components | lysine racemase | ||||||
Keywords | ISOMERASE / PLP binding / Racemization | ||||||
Function / homology | Function and homology information lysine racemase / alanine metabolic process / lysine racemase activity / alanine racemase activity / periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | Proteus mirabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Wang, W.C. / Wu, H.M. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants Authors: Wu, H.M. / Kuan, Y.C. / Chu, C.H. / Hsu, W.H. / Wang, W.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dza.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dza.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dza_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dza_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 4dza_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 4dza_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/4dza ftp://data.pdbj.org/pub/pdb/validation_reports/dz/4dza | HTTPS FTP |
-Related structure data
Related structure data | 4dyjSC 4fs9C 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: 45192.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: BCRC10725 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M4GGR9*PLUS, lysine racemase |
---|---|
#2: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Sodium-acetate, 0.05M Lithium-chloride, 29% PEG8000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 20, 2010 |
Radiation | Monochromator: a double-crystal monochromator and a horizontal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→30 Å / Num. all: 49586 / Num. obs: 39932 / % possible obs: 80.5 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.74→1.8 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DYJ Resolution: 1.74→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.851 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.209 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.741→1.786 Å / Total num. of bins used: 20
|