+Open data
-Basic information
Entry | Database: PDB / ID: 4p3k | ||||||
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Title | Structure of ancestral PyrR protein (PLUMPyrR) | ||||||
Components | Ancestral PyrR protein (Plum) | ||||||
Keywords | UNKNOWN FUNCTION / RNA binding proteins / reconstructed amino acid sequence | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 4p3k.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p3k.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 4p3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p3k_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 4p3k_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 4p3k_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 4p3k_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/4p3k ftp://data.pdbj.org/pub/pdb/validation_reports/p3/4p3k | HTTPS FTP |
-Related structure data
Related structure data | 4p80C 4p81C 4p82C 4p83C 4p84C 4p86C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20082.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Bacteria (eubacteria) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 40% PEG-300, 0.1M Tris pH 7.0, 5% PEG-1000 |
-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 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.86 Å / Num. obs: 20089 / % possible obs: 99 % / Redundancy: 6.7 % / Net I/σ(I): 11.5 |
-Processing
Software | Name: REFMAC / Version: 5.8.0069 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.199 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.106 / 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: 28.516 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→42.86 Å
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Refine LS restraints |
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