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Open data
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Basic information
Entry | Database: PDB / ID: 4p84 | ||||||
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Title | Structure of engineered PyrR protein (VIOLET PyrR) | ||||||
![]() | Bifunctional protein PyrR | ||||||
![]() | TRANSFERASE / RNA binding proteins / reconstructed amino acid sequence | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A. | ||||||
![]() | ![]() Title: Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Authors: Perica, T. / Kondo, Y. / Tiwari, S.P. / McLaughlin, S.H. / Kemplen, K.R. / Zhang, X. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.8 KB | Display | ![]() |
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Full document | ![]() | 448.3 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p3kC ![]() 4p80C ![]() 4p81C ![]() 4p82C ![]() 4p83C ![]() 4p86C ![]() 1a3cS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20123.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% PEG-600, 10% glycerol, 0.1M Tris pH 7.0, 0.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.55 Å / Num. obs: 8535 / % possible obs: 98.4 % / Redundancy: 2.6 % / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.2 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1a3c Resolution: 2.2→42.55 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.863 / SU B: 8.39 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.186 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→42.55 Å
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Refine LS restraints |
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