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- PDB-2pxd: Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recogni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pxd | ||||||
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Title | Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle | ||||||
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![]() | SIGNALING PROTEIN/RNA / GU PAIR / HEXAMINE / RNA PHASING / RNA / CATION BINDING / SIGNALING PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Keel, A.Y. / Rambo, R.P. / Batey, R.T. / Kieft, J.S. | ||||||
![]() | ![]() Title: A General Strategy to Solve the Phase Problem in RNA Crystallography. Authors: Keel, A.Y. / Rambo, R.P. / Batey, R.T. / Kieft, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.6 KB | Display | ![]() |
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PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.7 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pxbC ![]() 2pxeC ![]() 2pxfC ![]() 2pxkC ![]() 2pxlC ![]() 2pxpC ![]() 2pxqC ![]() 2pxtC ![]() 2pxuC ![]() 2pxvC ![]() 1dulS 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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Components
#1: RNA chain | Mass: 15885.515 Da / Num. of mol.: 1 / Fragment: DOMAIN IV / Mutation: C132G, U133G, A175U, G176U / Source method: obtained synthetically / Details: synthetic |
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#2: Protein | Mass: 12336.646 Da / Num. of mol.: 1 / Fragment: C TERMINAL DOMAIN (RESIDUES 328-432) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-NCO / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20Mm NaOH-MES pH 5.6, 200mM KCl, 10% Isopropanol, 5mM Cobalt Hexamine, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.93 Å / Num. obs: 22094 / % possible obs: 99.6 % / Redundancy: 4.11 % / Rmerge(I) obs: 0.15 / Χ2: 0.96 / Net I/σ(I): 5.2 / Scaling rejects: 687 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.2 / Num. measured all: 8183 / Num. unique all: 2194 / Χ2: 0.99 / % possible all: 98.3 |
-Phasing
Phasing MR | Cor.coef. Fo:Fc: 0.864 / Packing: 0.388
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1DUL Resolution: 2→50 Å / σ(F): 0
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Solvent computation | Bsol: 300 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Xplor file |
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