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- PDB-3gcm: Crystal Structure of E. coli polynucleotide phosphorylase bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gcm | ||||||
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Title | Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E | ||||||
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![]() | transferase / protein binding / Protein-RNA complex / Cytoplasm / Nucleotidyltransferase / RNA-binding / Transferase / Hydrolase / transferase - protein binding COMPLEX | ||||||
Function / homology | ![]() ribonuclease E / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nurmohamed, S. / Luisi, B.L. | ||||||
![]() | ![]() Title: Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Authors: Nurmohamed, S. / Vaidialingam, B. / Callaghan, A.J. / Luisi, B.F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 350.1 KB | Display | ![]() |
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PDB format | ![]() | 281.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 68.8 KB | Display | |
Data in CIF | ![]() | 98.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gllC ![]() 3gmeC ![]() 3h1cC ![]() 1e3hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 59657.812 Da / Num. of mol.: 3 / Fragment: residues 1-549 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A7ZS61, polyribonucleotide nucleotidyltransferase #2: Protein/peptide | Mass: 4340.687 Da / Num. of mol.: 3 Fragment: RNase E recognition microdomain, residues 1021-1061 Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli References: UniProt: A7ZKI9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 4 types, 898 molecules ![](data/chem/img/FLC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FLC / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2 M ammonium hydrogen citrate, 17 % w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2006 / Details: Monochromator |
Radiation | Monochromator: horizontally diffracting silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 102846 / Num. obs: 97645 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 27.176 Å2 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1E3H Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.883 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.212 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.176 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.563 Å / Total num. of bins used: 20
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