+Open data
-Basic information
Entry | Database: PDB / ID: 1p9y | ||||||
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Title | Ribosome binding of E. coli Trigger Factor mutant F44L. | ||||||
Components | Trigger factor | ||||||
Keywords | ISOMERASE / ALPHA-BETA PROTEIN | ||||||
Function / homology | Function and homology information 'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Kristensen, O. / Gajhede, M. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Chaperone binding at the ribosomal exit tunnel. Authors: Kristensen, O. / Gajhede, M. #1: Journal: Nature / Year: 2002 Title: L23 protein functions as a chaperone docking site on the ribosome. Authors: Kramer, G. / Rauch, T. / Rist, W. / Vorderwulbecke, S. / Patzelt, H. / Schulze-Specking, A. / Ban, N. / Deuerling, E. / Bukau, B. #2: Journal: J.Mol.Biol. / Year: 2003 Title: Localization of the Trigger Factor Binding Site on the Ribosomal 50S Subunit. Authors: Blaha, G. / Wilson, D.N. / Stoller, G. / Fischer, G. / Willumeit, R. / Nierhaus, K.H. #3: Journal: J.Mol.Biol. / Year: 2003 Title: Interaction of Trigger Factor with the Ribosome. Authors: Maier, R. / Eckert, B. / Scholz, C. / Lilie, H. / Schmid, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9y.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9y.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9y ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9y | HTTPS FTP |
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-Related structure data
Related structure data | 1omsSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Each of the separate chains A and B represent a biological relevant unit. |
-Components
#1: Protein | Mass: 13330.205 Da / Num. of mol.: 2 / Fragment: Ribosome binding domain / Mutation: F44L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TIG / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A850, peptidylprolyl isomerase #2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 44.95 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 2000 MME, AMMONIUM SULFATE, SODIUM ACETATE, TRIS, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.12 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 13, 2001 |
Radiation | Monochromator: Bendable asymmetrically cut Si(111) crystal in combination with vertically focusing cylindrical mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. all: 14381 / Num. obs: 14381 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1366 / Rsym value: 0.201 / % possible all: 96.7 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OMS Resolution: 2.15→35.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 348074.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Refinement was vased on the "MLF"target function and strong NCS restraints were used THROUGHOUT. Used all data in the ultimate brief refinement cycle against a standard crystallographic target: R-FACTOR(ALL).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2016 Å2 / ksol: 0.382659 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→35.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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