+Open data
-Basic information
Entry | Database: PDB / ID: 2f5m | ||||||
---|---|---|---|---|---|---|---|
Title | Cross-linked barnase soaked in bromo-ethanol | ||||||
Components | Ribonuclease | ||||||
Keywords | HYDROLASE / DENATURATION / LYSOZYME / BARNASE / CROSS-LINKED CRYSTALS / GLUTARALDEHYDE / UREA / THIOUREA / BROMOETHANOL | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Prange, T. / Salem, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2006 Title: On the edge of the denaturation process: Application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations. Authors: Salem, M. / Mauguen, Y. / Prange, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2f5m.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2f5m.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 2f5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5m ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5m | HTTPS FTP |
---|
-Related structure data
Related structure data | 2f2nC 2f30C 2f4aC 2f4gC 2f4ySC 2f56C 2f5wC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12199.515 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PMJ1002 / Production host: Escherichia coli (E. coli) References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: FROM AMMONIUM SULFATE, PROTEIN =20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 26, 2002 / Details: CURVATED MULTILAYER MIRROR |
Radiation | Monochromator: CURVATED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→9.5 Å / Num. all: 22360 / Num. obs: 20696 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.949→2.1 Å / Mean I/σ(I) obs: 9.7 / % possible all: 81.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2F4Y Resolution: 1.95→9.5 Å / Num. parameters: 11187 / Num. restraintsaints: 10765 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 2508 / Occupancy sum non hydrogen: 2796 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→9.5 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell |
|