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- PDB-2vrt: Crystal Structure of E. coli RNase E possessing M1 RNA fragments ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vrt | ||||||
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Title | Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain | ||||||
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![]() | HYDROLASE / RNA PROCESSING / M1 RNA / RNASE P / NUCLEASE / CYTOPLASM / RNA-BINDING / RNA TURNOVER / ENDONUCLEASE | ||||||
Function / homology | ![]() regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Garman, E.F. / Martick, M. / Scott, W.G. / Luisi, B.F. | ||||||
![]() | ![]() Title: The Crystal Structure of the Escherichia Coli Rnase E Apoprotein and a Mechanism for RNA Degradation. Authors: Koslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Garman, E.F. / Martick, M. / Scott, W.G. / Luisi, B.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "DB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 668.4 KB | Display | ![]() |
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PDB format | ![]() | 555.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vmkC ![]() 2bx2S S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 57280.043 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: RNA chain | Mass: 567.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: RNA chain | Mass: 912.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 55.5 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 10% PEG 4000, 100 MM (NH4)2SO4, AND 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: QUANTUM / Detector: CCD / Date: Mar 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→79.5 Å / Num. obs: 33891 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BX2 Resolution: 3.5→24.98 Å / Cor.coef. Fo:Fc: 0.805 / Cor.coef. Fo:Fc free: 0.768 / SU B: 117.646 / SU ML: 1.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.838 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO OUT OF THE FOUR EXPECTED S1 DOMAINS (RESIDUES 36-118, CHAINS B AND C) ARE MISSING AND PRESUMED TO BE EITHER ABSENT OR DISORDERED IN THE CRYSTAL.
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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: 108.89 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→24.98 Å
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Refine LS restraints |
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