+Open data
-Basic information
Entry | Database: PDB / ID: 1t6y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ADP, AMP, and FMN bound TM379 | ||||||
Components | riboflavin kinase/FMN adenylyltransferase | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / Crystal / FAD Synthetase / ADP / AMP / FMN / X-ray crystallography / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information riboflavin metabolic process / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shin, D.H. / Wang, W. / Kim, R. / Yokota, H. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ADP bound FAD synthetase Authors: Shin, D.H. / Wang, W. / Kim, R. / Yokota, H. / Kim, S.-H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t6y.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t6y.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6y ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6y | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33665.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PSJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZW1 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, sodium citrate, glycerol, propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2001 / Details: Monochromator |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 16364 / Num. obs: 16249 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 138.9 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 97.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 791662.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.2415 Å2 / ksol: 0.294702 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.92 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|