+Open data
-Basic information
Entry | Database: PDB / ID: 2hyb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Hexameric DsrEFH | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / DsrE / DsrF / DsrH / Sulfur / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC | ||||||
Function / homology | Function and homology information Transferases; Transferring sulfur-containing groups; Sulfurtransferases / tRNA wobble position uridine thiolation / sulfur oxidation / sulfurtransferase activity / tRNA processing / cytoplasm Similarity search - Function | ||||||
Biological species | Allochromatium vinosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Shin, D.H. / Connie, H. / Schulte, A. / Dahl, C. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of hexameric DsrEFH Authors: Shin, D.H. / Connie, H. / Schulte, A. / Dahl, C. / Kim, R. / Kim, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hyb.cif.gz | 438.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hyb.ent.gz | 355.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/2hyb ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hyb | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14607.287 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrE / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O87896, Transferases; Transferring sulfur-containing groups; Sulfurtransferases #2: Protein | Mass: 15606.442 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrF / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87897 #3: Protein | Mass: 11094.615 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: dsrH / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87898 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.67 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20mg/ml protein, 0.1M Bis-Tris pH5.5 0.2M Lithium Sulfate 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. all: 74225 / Num. obs: 72592 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.3 Å2 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 81.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.5→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 62422.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.7916 Å2 / ksol: 0.295294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|