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Yorodumi- PDB-4kji: Novel re-arrangement of an RsmA/cSRa family protein to create a s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kji | ||||||
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Title | Novel re-arrangement of an RsmA/cSRa family protein to create a structurally distinct new RNA-binding family member | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / BETA BARREL / BETA-BARREL / POST-TRANSCRIPTIONAL REGULATION / RNA BINDING / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information regulation of carbohydrate metabolic process / mRNA catabolic process / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Li, C. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural Rearrangement in an RsmA/CsrA Ortholog of Pseudomonas aeruginosa Creates a Dimeric RNA-Binding Protein, RsmN. Authors: Morris, E.R. / Hall, G. / Li, C. / Heeb, S. / Kulkarni, R.V. / Lovelock, L. / Silistre, H. / Messina, M. / Camara, M. / Emsley, J. / Williams, P. / Searle, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kji.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kji.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kji_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 4kji_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 4kji_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4kji_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/4kji ftp://data.pdbj.org/pub/pdb/validation_reports/kj/4kji | HTTPS FTP |
-Related structure data
Related structure data | 4krwC 1vpzS 2jppS S: Starting model for refinement 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
#1: Protein | Mass: 8768.108 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA14_68470, rsmN / Plasmid: pME600 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q02EI1, UniProt: A0A0H2ZIZ8*PLUS #2: RNA chain | Mass: 5191.176 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence occurs naturally in Pseudomonas aeruginosa |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Method: evaporation / pH: 4.5 Details: 0.08M Mg(OAc)2, 0.1M NaOAc pH 4.5, 4% benzamidine HCl, 4% PEG 8000., EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.57 Å / Num. obs: 5917 / Redundancy: 8.8 % / Rmerge(I) obs: 0.085 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 18.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1vpz for protein and 2JPP for RNA Resolution: 3.2→29.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 29.686 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 109.22 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→29.56 Å
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Refine LS restraints |
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