+Open data
-Basic information
Entry | Database: PDB / ID: 2igi | ||||||
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Title | Crystal Structure of E. coli Oligoribonuclease | ||||||
Components | Oligoribonuclease | ||||||
Keywords | HYDROLASE / RNase / Exoribonuclease / ribonuclease / exonuclease / nuclease / mRNA decay | ||||||
Function / homology | Function and homology information oligoribonucleotidase activity / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / single-stranded DNA 3'-5' DNA exonuclease activity / RNA catabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zuo, Y. / Malhotra, A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia coli Authors: Fiedler, T.J. / Zuo, Y. / Malhotra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2igi.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2igi.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 2igi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2igi_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 2igi_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 2igi_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2igi_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2igi ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igi | HTTPS FTP |
-Related structure data
Related structure data | 1ytaSC 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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Details | The asymmetric unit has two monomers, which form the biological assembly. |
-Components
#1: Protein | Mass: 20709.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: orn / Plasmid: pUC19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A784, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-ACY / #5: Water | ChemComp-HOH / | |
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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: 3.25 Å3/Da / Density % sol: 62.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0 M Sodium Acetate, 0.05 M Cadmium Sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 57187 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 8.3 / Num. unique all: 5777 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YTA Resolution: 1.7→29.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 505307.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3056 Å2 / ksol: 0.376005 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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