[English] 日本語
Yorodumi- PDB-3wdk: Crystal structure of 4-phosphopantoate-beta-alanine ligase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wdk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate | ||||||
Components | 4-phosphopantoate--beta-alanine ligase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information 4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Authors: Kishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wdk.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wdk.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 3wdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wdk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wdk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3wdk_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 3wdk_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdk ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29891.600 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1686 / Production host: Escherichia coli (E. coli) References: UniProt: Q5JIZ8, 4-phosphopantoate-beta-alanine ligase #2: Chemical | ChemComp-PTJ / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 50% Tacsimate, 1% PEG 3350, 100mM sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 21, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 64483 / Num. obs: 64483 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.2 Å2 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4635031.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.676 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.49 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|