+Open data
-Basic information
Entry | Database: PDB / ID: 1w2b | ||||||
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Title | Trigger Factor ribosome binding domain in complex with 50S | ||||||
Components |
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Keywords | RIBOSOME / RIBOSOME_ASSOCIATED FACTORS / CHAPERONE / NASCENT CHAIN / COTRANSLATIONAL FOLDING / RNA-BINDING / RIBOSOMAL PROTEIN | ||||||
Function / homology | Function and homology information 'de novo' cotranslational protein folding / stress response to copper ion / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...'de novo' cotranslational protein folding / stress response to copper ion / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / peptidylprolyl isomerase / maturation of SSU-rRNA / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / protein transport / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / nucleotide binding / DNA binding / zinc ion binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) HALOARCULA MARISMORTUI (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Ferbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins Authors: Ferbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JC" 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. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w2b.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1w2b.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1w2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w2b_validation.pdf.gz | 663.1 KB | Display | wwPDB validaton report |
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Full document | 1w2b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1w2b_validation.xml.gz | 167.3 KB | Display | |
Data in CIF | 1w2b_validation.cif.gz | 299.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w2b ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w2b | HTTPS FTP |
-Related structure data
Related structure data | 1w26C 1jj2S 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
-RNA chain , 2 types, 2 molecules 09
#1: RNA chain | Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 3377779 |
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#5: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 3377779 |
+50S RIBOSOMAL PROTEIN ... , 26 types, 26 molecules 12ABCDEFGHIJKLMNOPQRTUVWXY
-Protein , 1 types, 1 molecules 5
#4: Protein | Mass: 15837.027 Da / Num. of mol.: 1 Fragment: N-TERMINAL RIBOSOME BINDING FRAGMENT, RESIDUES 1-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: GenBank: 147989, UniProt: P0A850*PLUS |
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-RIBOSOMAL PROTEIN ... , 2 types, 2 molecules SZ
#24: Protein | Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10972 |
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#31: Protein | Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32410 |
-Non-polymers , 6 types, 8119 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / #37: Water | ChemComp-HOH / | |
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-Details
Sequence details | NUMBERING OF L23P DIFFERS FROM THE GENE DERIVED SEQUENCE BY 1 BECAUSE OF THE MISSING INITIAL ...NUMBERING OF L23P DIFFERS FROM THE GENE DERIVED SEQUENCE BY 1 BECAUSE OF THE MISSING INITIAL METHIONINE |
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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: 3.08 Å3/Da / Density % sol: 55 % |
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Crystal grow | Details: PEG 6000, KCL, NH4CL, MGCL2, CDCL2, POTASSIUM ACETATE, TRIS-MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 241873 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.258 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JJ2 Resolution: 3.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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