+Open data
-Basic information
Entry | Database: PDB / ID: 2ix0 | ||||||
---|---|---|---|---|---|---|---|
Title | RNase II | ||||||
Components | EXORIBONUCLEASE 2 | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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 |
| ||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ix0.cif.gz | 151 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ix0.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ix0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ix0_validation.pdf.gz | 736.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ix0_full_validation.pdf.gz | 753 KB | Display | |
Data in XML | 2ix0_validation.xml.gz | 27 KB | Display | |
Data in CIF | 2ix0_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ix0 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ix0 | HTTPS FTP |
-Related structure data
Related structure data | 2ix1SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 74598.945 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-644 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 |
---|---|
#2: Chemical | ChemComp-C5P / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Sequence 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 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 8-12 MG/ML 3% GLYCEROL 1 MM MGCL2 100 MM KCL AND 100 MM TRIS-HCL PH 8.0, AND 1.5 MICRO-L OF WELL SOLUTION, 22 % PEG ...Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 8-12 MG/ML 3% GLYCEROL 1 MM MGCL2 100 MM KCL AND 100 MM TRIS-HCL PH 8.0, AND 1.5 MICRO-L OF WELL SOLUTION, 22 % PEG 4K, 0.6M CA ACETATE AND 0.1M TRIS-HCL PH 8.5, AT 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.975 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→43.94 Å / Num. obs: 31569 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.44→2.53 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.2 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IX1 Resolution: 2.44→62.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.3 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DISOREDERED N-TERMINUS UNTIL RESIDUE 4 AND LOOP BETWEEN REIDUES 30-33 AND 67-70 WERE NOT MODELLED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 39.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→62.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|