+Open data
-Basic information
Entry | Database: PDB / ID: 2ix1 | ||||||
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Title | RNase II D209N mutant | ||||||
Components |
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Keywords | HYDROLASE / S1 / RNA / CSD / RNB / NUCLEASE / RNASE II / RNA- BINDING / EXONUCLEASE | ||||||
Function / homology | Function and homology information exoribonuclease II / exoribonuclease II activity / mRNA catabolic process / 3'-5' exonuclease activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) ESCHERICHIA COLI BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.74 Å | ||||||
Authors | Frazao, C. / McVey, C.E. / Amblar, M. / Barbas, A. / Vonrhein, C. / Arraiano, C.M. / Carrondo, M.A. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Unravelling the Dynamics of RNA Degradation by Ribonuclease II and its RNA-Bound Complex Authors: Frazao, C. / Mcvey, C.E. / Amblar, M. / Barbas, A. / Vonrhein, C. / Arraiano, C.M. / Carrondo, M.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Expression, Purification, Crystallization and Preliminary Diffraction Data Characterization of Escherichia Coli Ribonuclease II (Rnase II) Authors: Mcvey, C.E. / Amblar, M. / Barbas, A. / Cairrao, F. / Coelho, R. / Romao, C. / Arraiano, C.M. / Carrondo, M.A. / Frazao, C. #2: Journal: J.Mol.Biol. / Year: 2006 Title: Characterization of the Functional Domains of Escherichia Coli Rnase II. Authors: Amblar, M. / Barbas, A. / Fialho, A.M. / Arraiano, C.M. #3: Journal: Mol.Microbiol. / Year: 1993 Title: DNA Sequencing and Expression of the Gene Rnb Encoding Escherichia Coli Ribonuclease II Authors: Zilhao, R. / Camelo, L. / Arraiano, C.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ix1.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ix1.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ix1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ix1 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ix1 | HTTPS FTP |
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-Related 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: 74683.062 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-644 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: C600 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30850, exoribonuclease II | ||
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#2: RNA chain | Mass: 4234.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CHAIN B CONSISTS OF A 13 NUCLEOTIDE RNA FRAGMENT TRAPPED BY THE INACTIVE RNASE II D209N MUTANT DURING PURIFICATION. IT WAS PUTATIVELY MODELLED AS A POLY-ADENINE OLIGONUCLEOTIDE. Source: (natural) ESCHERICHIA COLI BL21(DE3) (bacteria) | ||
#3: Chemical | ChemComp-MG / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | N-TERMINAL HIS-TAGGED PROTEIN, WHERE THE FIRST 5 RESIDUES, MFQDN, ARE REPLACED BY ...N-TERMINAL HIS-TAGGED PROTEIN, WHERE THE FIRST 5 RESIDUES, MFQDN, ARE REPLACED BY MGSSHHHHHH | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 20 MM TRIS-HCL PH 8, 150 MM NACL, 10% GLYCEROL AND 1 MM DTT, AND 1.5 MICRO-L OF WELL SOLUTION,2.4 M SODIUM MALONATE PH 6.0, AT 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→51 Å / Num. obs: 30737 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.74→2.85 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.74→29.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 21.858 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED C-TERMINUS WAS NOT MODELLED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→29.3 Å
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Refine LS restraints |
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