+Open data
-Basic information
Entry | Database: PDB / ID: 2z70 | ||||||
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Title | E.coli RNase 1 in complex with d(CGCGATCGCG) | ||||||
Components |
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Keywords | HYDROLASE / ribonuclease / Endonuclease | ||||||
Function / homology | Function and homology information Enterobacter ribonuclease / Enterobacter ribonuclease activity / ribonuclease T2 activity / RNA catabolic process / outer membrane-bounded periplasmic space / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Martinez-Rodriguez, S. / Loris, R. / Messens, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli Authors: Rodriguez, S.M. / Panjikar, S. / Van Belle, K. / Wyns, L. / Messens, J. / Loris, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z70.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z70.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2z70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z70 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z70 | HTTPS FTP |
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-Related structure data
Related structure data | 2pqxS S: Starting model for refinement |
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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: DNA chain | Mass: 2123.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis |
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#2: Protein | Mass: 27192.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rna, rnsA / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21338, EC: 3.1.27.6 |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 20% PEG8000, 0.1M Sodium acetate, 1mM MgCl2, 0.1M MES, pH6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8125 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. all: 28734 / Num. obs: 28734 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 4.34 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2813 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PQX Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.197 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.326 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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