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Open data
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Basic information
Entry | Database: PDB / ID: 2f5m | ||||||
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Title | Cross-linked barnase soaked in bromo-ethanol | ||||||
![]() | Ribonuclease | ||||||
![]() | HYDROLASE / DENATURATION / LYSOZYME / BARNASE / CROSS-LINKED CRYSTALS / GLUTARALDEHYDE / UREA / THIOUREA / BROMOETHANOL | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prange, T. / Salem, M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.7 KB | Display | ![]() |
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PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f2nC ![]() 2f30C ![]() 2f4aC ![]() 2f4gC ![]() 2f4ySC ![]() 2f56C ![]() 2f5wC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12199.515 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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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 |
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Diffraction source | Source: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2F4Y Resolution: 1.95→9.5 Å / Num. parameters: 11187 / Num. restraintsaints: 10765 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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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
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Refine LS restraints |
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LS refinement shell |
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