+Open data
-Basic information
Entry | Database: PDB / ID: 4p83 | ||||||
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Title | Structure of engineered PyrR protein (PURPLE PyrR) | ||||||
Components | Engineered PyrR protein (Purple) | ||||||
Keywords | TRANSCRIPTION / RNA binding proteins / reconstructed amino acid sequence | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / URIDINE-5'-MONOPHOSPHATE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Perica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A. | ||||||
Citation | Journal: Science / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p83.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p83.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 4p83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p83_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4p83_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4p83_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 4p83_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/4p83 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/4p83 | HTTPS FTP |
-Related structure data
Related structure data | 4p3kC 4p80C 4p81C 4p82C 4p84C 4p86C 1a3cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 20281.174 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Bacteria (eubacteria) #2: Chemical | ChemComp-U5P / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15% PEG 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→53.59 Å / Num. obs: 29162 / % possible obs: 99 % / Redundancy: 11.9 % / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.166 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a3c Resolution: 2.5→74.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.453 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.278 / 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: 50.048 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→74.5 Å
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Refine LS restraints |
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