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Yorodumi- PDB-2yjv: Crystal structure of E. coli regulator of ribonuclease activity A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yjv | ||||||
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Title | Crystal structure of E. coli regulator of ribonuclease activity A (RraA) bound to fragment of DEAD-box protein RhlB | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR/HYDROLASE / HYDROLASE INHIBITOR-HYDROLASE COMPLEX / DEAD BOX RNA HELICASES | ||||||
Function / homology | Function and homology information negative regulation of RNA catabolic process / ribonuclease inhibitor activity / protein homotrimerization / endoribonuclease inhibitor activity / enzyme binding / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pietras, Z. / Hardwick, S.W. / Luisi, B.F. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2013 Title: Potential regulatory interactions of Escherichia coli RraA protein with DEAD-box helicases. Authors: Pietras, Z. / Hardwick, S.W. / Swiezewski, S. / Luisi, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yjv.cif.gz | 350.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yjv.ent.gz | 287.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yjv_validation.pdf.gz | 513.3 KB | Display | wwPDB validaton report |
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Full document | 2yjv_full_validation.pdf.gz | 556.2 KB | Display | |
Data in XML | 2yjv_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 2yjv_validation.cif.gz | 90.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjv ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjv | HTTPS FTP |
-Related structure data
Related structure data | 2yjtC 1q5xS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 17371.264 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A8R0 #2: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: DNA helicase #3: Water | ChemComp-HOH / | Sequence details | CHAINS M AND N ARE PEPTIDE OF SEQUENCE YRLTRPRTGNGPRRTGAPRNRRRSG WHICH CORRESPONDS TO RESIDUES 398- ...CHAINS M AND N ARE PEPTIDE OF SEQUENCE YRLTRPRTGN | |
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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: 2.58 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. ...Details: CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. PLATES WERE THEN IMMEDIATELY TRANSFERRED TO 16 C. CRYSTALS WERE DIRECTLY FLASH FROZEN IN LIQUID NITROGEN. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 7, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→63.53 Å / Num. obs: 47500 / % possible obs: 98 % / Observed criterion σ(I): 6 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q5X Resolution: 2.8→122.62 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.997 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 57.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→122.62 Å
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Refine LS restraints |
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