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Yorodumi- PDB-2pxd: Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recogni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pxd | ||||||
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Title | Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle | ||||||
Components |
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Keywords | SIGNALING PROTEIN/RNA / GU PAIR / HEXAMINE / RNA PHASING / RNA / CATION BINDING / SIGNALING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Keel, A.Y. / Rambo, R.P. / Batey, R.T. / Kieft, J.S. | ||||||
Citation | Journal: Structure / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pxd.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pxd.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/2pxd ftp://data.pdbj.org/pub/pdb/validation_reports/px/2pxd | HTTPS FTP |
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-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 (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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-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.) Escherichia coli (E. coli) / Gene: ffh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P0AGD7 |
#3: Chemical | ChemComp-NCO / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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