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Open data
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Basic information
Entry | Database: PDB / ID: 1yvs | ||||||
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Title | Trimeric domain swapped barnase | ||||||
![]() | BARNASE | ||||||
![]() | ENDONUCLEASE / RIBONUCLEASE / DOMAIN SWAPPED / TRIMER | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zegers, I. / Wyns, L. | ||||||
![]() | ![]() Title: Trimeric domain-swapped barnase. Authors: Zegers, I. / Deswarte, J. / Wyns, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.9 KB | Display | ![]() |
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PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.1 KB | Display | ![]() |
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Full document | ![]() | 430.1 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1brnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12398.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.9 Å / % possible obs: 98 % / Redundancy: 22 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.069 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.158 / % possible all: 95 |
Reflection | *PLUS Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.158 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BRN Resolution: 2.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR |F| GREATER THAN 3 ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR |F| GREATER THAN 3 SIGMA(F), THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL-93. THE FREE R VALUE WAS MONITORED IN THE FIRST STEPS OF REFINEMENT. THE MODEL WAS FINALLY REFINED USING ALL DATA.
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Displacement parameters | Biso mean: 29.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.238 |