+Open data
-Basic information
Entry | Database: PDB / ID: 6by1 | |||||||||
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Title | E. coli pH03H9 complex | |||||||||
Components |
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Keywords | RIBOSOME / mRNA / tRNA / helicase | |||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å | |||||||||
Authors | Amiri, H. / Noller, H.F. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Rna / Year: 2019 Title: Structural evidence for product stabilization by the ribosomal mRNA helicase. Authors: Amiri, H. / Noller, H.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6by1.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6by1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6by1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6by1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6by1_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6by1_validation.xml.gz | 696.3 KB | Display | |
Data in CIF | 6by1_validation.cif.gz | 1024 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/6by1 ftp://data.pdbj.org/pub/pdb/validation_reports/by/6by1 | HTTPS FTP |
-Related structure data
Related structure data | 4v9dS S: Starting model for refinement |
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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
-RNA chain , 5 types, 13 molecules AABACADACBDBAVAYAWBVBWAXBX
#1: RNA chain | Mass: 499360.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1126835768 #2: RNA chain | Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 687670942 #3: RNA chain | Mass: 38177.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1266940032 #4: RNA chain | Mass: 24483.572 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1275521620 #36: RNA chain | Mass: 14995.027 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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+50S ribosomal protein ... , 31 types, 61 molecules CCDCCDDDCEDECFDFCGDGCHDHC5CIDICJDJCKDKCLDLCMDMCNDNCODOCPDPCQ...
-30S ribosomal protein ... , 19 types, 38 molecules ABBBACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBP...
#37: Protein | Mass: 25015.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V0 #38: Protein | Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V3 #39: Protein | Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V8 #40: Protein | Mass: 15804.282 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W1 #41: Protein | Mass: 11669.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358 #42: Protein | Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02359 #43: Protein | Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W7 #44: Protein | Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7X3 #45: Protein | Mass: 11196.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R5 #46: Protein | Mass: 12487.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R9 #47: Protein | Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S3 #48: Protein | Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S9 #49: Protein | Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG59 #50: Protein | Mass: 10290.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ4 #51: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T3 #52: Protein | Mass: 9263.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG63 #53: Protein | Mass: 6466.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T7 #54: Protein | Mass: 9057.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U3 #55: Protein | Mass: 9506.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U7 |
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-Non-polymers , 3 types, 4365 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: 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: 3.23 Å3/Da / Density % sol: 61.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 2000, PEP629, potassium thiocyanate, tris acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.94→59.994 Å / Num. obs: 501982 / % possible obs: 99.9 % / Redundancy: 8.172 % / Biso Wilson estimate: 137.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.571 / Rrim(I) all: 0.609 / Χ2: 0.904 / Net I/σ(I): 3.58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4V9D Resolution: 3.94→59.994 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 366.01 Å2 / Biso mean: 136.3538 Å2 / Biso min: 20.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.94→59.994 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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