+Open data
-Basic information
Entry | Database: PDB / ID: 7asm | ||||||
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Title | Staphylococcus aureus 50S after 30 minutes incubation at 37C | ||||||
Components |
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Keywords | RIBOSOME / H68 / translation / protein synthesis | ||||||
Function / homology | Function and homology information large ribosomal subunit / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å | ||||||
Authors | Cimicata, G. / Bashan, A. / Yonath, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Staphylococcus aureus 50S after 30 minutes incubation a 37C Authors: Cimicata, G. / Bashan, A. / Yonath, A. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7asm.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7asm.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 7asm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7asm_validation.pdf.gz | 1019.3 KB | Display | wwPDB validaton report |
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Full document | 7asm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7asm_validation.xml.gz | 122.7 KB | Display | |
Data in CIF | 7asm_validation.cif.gz | 219.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7asm ftp://data.pdbj.org/pub/pdb/validation_reports/as/7asm | HTTPS FTP |
-Related structure data
Related structure data | 11900MC 7asnC 7asoC 7aspC M: map data used to model this data 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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-Components
+50S ribosomal protein ... , 27 types, 27 molecules NECGHJKMOPRSTUW3124DFIQVXZL
-RNA chain , 2 types, 2 molecules AB
#3: RNA chain | Mass: 946738.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ...Details: GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUGGGGAGCUGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUGAAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCCCUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUGUACGGAGUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACUCUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAACCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUGAUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGAGUCUUCGAGUCGUUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGGUAACUUCGGGAGAAGGGGUGCUCUUUAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAAGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) |
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#4: RNA chain | Mass: 36974.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: GenBank: 1434110260 |
-Non-polymers , 1 types, 1 molecules
#30: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 50S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#29 / Source: NATURAL |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198422 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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