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70S ribosome from Staphylococcus aureus

by single particle reconstruction, at 3.8 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-4050, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5li0
Title70S ribosome from Staphylococcus aureus
Descriptor(30S ribosomal protein ...) x 19
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME, pathogenic ribosome, bL31 B-type, ribosome
AuthorsKhusainov, I., Vicens, Q., Bochler, A., Grosse, F., Myasnikov, A., Menetret, J.F., Chicher, J., Marzi, S., Romby, P., Yusupova, G., Yusupov, M., Hashem, Y.
DateDeposition: 2016-07-13, Release: 2016-12-28
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-4050, Imaged by UCSF CHIMERA

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EMDB-4050

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Article
Citation - primary
ArticleNucleic Acids Res., Vol. 44, Issue 21, Page 10491-10504, Year 2016
TitleStructure of the 70S ribosome from human pathogen Staphylococcus aureus.
AuthorsIskander Khusainov, Quentin Vicens, Anthony Bochler, François Grosse, Alexander Myasnikov, Jean-François Ménétret, Johana Chicher, Stefano Marzi, Pascale Romby, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch 67400, France.
Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.
Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France.
Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch 67400, France
Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
LinksPubMed: 27906650, DOI: 10.1093/nar/gkw933, PMC: PMC5137454
Components
ID 1 : 16S ribosomal RNA
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight500464.406 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 1547
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksGenBank: 87201381, Sequence view
ID 2 : 30S ribosomal protein S2
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight29136.369 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 255
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FZ25, Sequence view
ID 3 : 30S ribosomal protein S3
Description30S ribosomal protein S3
Typepolypeptide(L)
Formula weight24143.867 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 217
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW12, Sequence view
ID 4 : 30S ribosomal protein S4
Description30S ribosomal protein S4
Typepolypeptide(L)
Formula weight22920.221 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 199
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXK6, Sequence view
ID 5 : 30S ribosomal protein S5
Description30S ribosomal protein S5
Typepolypeptide(L)
Formula weight17639.314 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 165
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW23, Sequence view
ID 6 : 30S ribosomal protein S6
Description30S ribosomal protein S6
Typepolypeptide(L)
Formula weight11368.879 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 96
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2G113, Sequence view
ID 7 : 30S ribosomal protein S7
Description30S ribosomal protein S7
Typepolypeptide(L)
Formula weight17167.736 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 150
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: P48940, Sequence view
ID 8 : 30S ribosomal protein S8
Description30S ribosomal protein S8
Typepolypeptide(L)
Formula weight14723.118 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 131
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW20, Sequence view
ID 9 : 30S ribosomal protein S9
Description30S ribosomal protein S9
Typepolypeptide(L)
Formula weight14440.450 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 128
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW39, Sequence view
ID 10 : 30S ribosomal protein S10
Description30S ribosomal protein S10
Typepolypeptide(L)
Formula weight11600.520 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 102
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q931G5, Sequence view
ID 11 : 30S ribosomal protein S11
Description30S ribosomal protein S11
Typepolypeptide(L)
Formula weight12562.294 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 118
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW31, Sequence view
ID 12 : 30S ribosomal protein S12
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight15131.598 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 135
NCBI taxonomy: ID:93062
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q5HID0, Sequence view
ID 13 : 30S ribosomal protein S13
Description30S ribosomal protein S13
Typepolypeptide(L)
Formula weight13487.543 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 119
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW30, Sequence view
ID 14 : 30S ribosomal protein S14 type Z
Description30S ribosomal protein S14 type Z
Typepolypeptide(L)
Formula weight7186.573 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 60
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW19, Sequence view
ID 15 : 30S ribosomal protein S15
Description30S ribosomal protein S15
Typepolypeptide(L)
Formula weight10503.135 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 88
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2G2Q1, Sequence view
ID 16 : 30S ribosomal protein S16
Description30S ribosomal protein S16
Typepolypeptide(L)
Formula weight10122.690 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 90
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FZ45, Sequence view
ID 17 : 30S ribosomal protein S17
Description30S ribosomal protein S17
Typepolypeptide(L)
Formula weight10065.691 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 86
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW15, Sequence view
ID 18 : 30S ribosomal protein S18
Description30S ribosomal protein S18
Typepolypeptide(L)
Formula weight8418.959 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 71
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2G111, Sequence view
ID 19 : 30S ribosomal protein S19
Description30S ribosomal protein S19
Typepolypeptide(L)
Formula weight9605.988 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 84
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW10, Sequence view
ID 20 : 30S ribosomal protein S20
Description30S ribosomal protein S20
Typepolypeptide(L)
Formula weight8708.018 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 80
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXY6, Sequence view
ID 21 : 23S ribosomal RNA
Description23S ribosomal RNA
Typepolyribonucleotide
Formula weight945058.562 Da
Number of molecules1
ID21
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 2918
Gene: ID:93061, Staphylococcus aureus (strain NCTC 8325)
Host: ID:93061, Staphylococcus aureus (strain NCTC 8325)
Seq type: Biological sequence
LinksGenBank: 87201381, Sequence view
ID 22 : 5S ribosomal RNA
Description5S ribosomal RNA
Typepolyribonucleotide
Formula weight36692.801 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 114
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksGenBank: 87201381, Sequence view
ID 23 : 50S ribosomal protein L2
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight29956.789 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 275
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: P60430, Sequence view
ID 24 : 50S ribosomal protein L3
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight23499.877 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 218
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW06, Sequence view
ID 25 : 50S ribosomal protein L4
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight21666.725 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 199
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW07, Sequence view
ID 26 : 50S ribosomal protein L5
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight18729.721 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 166
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW18, Sequence view
ID 27 : 50S ribosomal protein L6
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight18296.711 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 164
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW21, Sequence view
ID 28 : 50S ribosomal protein L13
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight16359.427 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 145
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW38, Sequence view
ID 29 : 50S ribosomal protein L14
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13157.342 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 122
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW16, Sequence view
ID 30 : 50S ribosomal protein L15
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight14193.304 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 131
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: P0A0F8, Sequence view
ID 31 : 50S ribosomal protein L16
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight15943.755 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 141
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW13, Sequence view
ID 32 : 50S ribosomal protein L17
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight13420.350 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 119
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW33, Sequence view
ID 33 : 50S ribosomal protein L18
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight13124.093 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 119
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW22, Sequence view
ID 34 : 50S ribosomal protein L19
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight12594.825 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 110
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FZ42, Sequence view
ID 35 : 50S ribosomal protein L20
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13459.919 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 116
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXQ1, Sequence view
ID 36 : 50S ribosomal protein L21
Description50S ribosomal protein L21
Typepolypeptide(L)
Formula weight11354.081 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 102
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXS8, Sequence view
ID 37 : 50S ribosomal protein L22
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight12328.358 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 112
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW11, Sequence view
ID 38 : 50S ribosomal protein L23
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight10380.100 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 89
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW08, Sequence view
ID 39 : 50S ribosomal protein L24
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight10976.878 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 100
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW17, Sequence view
ID 40 : General stress protein CTC
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10522.318 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 94
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2G0S0, Sequence view
ID 41 : 50S ribosomal protein L27
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight8911.099 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 82
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXT0, Sequence view
ID 42 : 50S ribosomal protein L28
Description50S ribosomal protein L28
Typepolypeptide(L)
Formula weight5312.262 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 46
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FZ60, Sequence view
ID 43 : 50S ribosomal protein L29
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7660.762 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 65
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW14, Sequence view
ID 44 : 50S ribosomal protein L30
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6305.308 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 57
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: P0A0G2, Sequence view
ID 45 : 50S ribosomal protein L31 type B
Description50S ribosomal protein L31 type B
Typepolypeptide(L)
Formula weight9737.912 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 84
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FWD8, Sequence view
ID 46 : 50S ribosomal protein L32
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight6397.427 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 56
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FZF1, Sequence view
ID 47 : 50S ribosomal protein L33 2
Description50S ribosomal protein L33 2
Typepolypeptide(L)
Formula weight4711.371 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 39
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FY22, Sequence view
ID 48 : 50S ribosomal protein L34
Description50S ribosomal protein L34
Typepolypeptide(L)
Formula weight5323.446 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 44
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FUQ0, Sequence view
ID 49 : 50S ribosomal protein L35
Description50S ribosomal protein L35
Typepolypeptide(L)
Formula weight6985.402 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 60
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FXQ0, Sequence view
ID 50 : 50S ribosomal protein L36
Description50S ribosomal protein L36
Typepolypeptide(L)
Formula weight4318.422 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 37
NCBI taxonomy: ID:93061
Organism scientific: Staphylococcus aureus (strain NCTC 8325)
LinksUniProt: Q2FW29, Sequence view
ID 51 : MAGNESIUM ION
DescriptionMAGNESIUM ION
Typenon-polymer
Formula weight24.305 Da
Number of molecules31
ID51
SourceMethod: Obtained synthetically
ID 52 : OXYGEN ATOM
DescriptionOXYGEN ATOM
Typenon-polymer
Formula weight15.999 Da
Number of molecules9
ID52
SourceMethod: Obtained synthetically
ID 53 : ZINC ION
DescriptionZINC ION
Typenon-polymer
Formula weight65.409 Da
Number of molecules1
ID53
SourceMethod: Obtained synthetically
ID 54 : water
Descriptionwater
Typewater
Formula weight18.015 Da
Number of molecules162
ID54
SourceMethod: Isolated from a natural source
Sample
Entity assembly
Entity id list1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
Name70S ribosome from Staphylococcus aureus
TypeRIBOSOME
Buffer
Specimen id1
Details5 mM Hepes-KOH pH 7.5 50 mM KCl 10 mM NH4Cl 10 mM Mg(OAc)2 1 mM DTT
PH7.5
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Grid materialCOPPER
Vitrification
Specimen id1
Chamber temperature277
Cryogen nameETHANE
Detailsblot force 5, blot waiting time 30 s
Humidity100
InstrumentFEI VITROBOT MARK IV
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeDARK FIELD
Image scans
Image recording id1
Frames per image17
Used frames per image2-8
Processing
3D reconstruction
Image processing id1
AlgorithmFOURIER SPACE
Num class averages8
Number of particles110000
Resolution3.8 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
3D fitting
Refinement ProtocolOTHER
Refinement SpaceREAL
Refine
Refine idELECTRON MICROSCOPY
Software
Ordinal1
Classificationrefinement
NamePHENIX
Versiondev_2341:
Download
PDB format
Allpdb5li0.ent.gz
pdb5li0.ent (uncompressed file)
Header onlypdb5li0.ent.gz
mmCIF format
mmCIF5li0.cif.gz
XML format
All5li0.xml.gz
No-atom5li0-noatom.xml.gz
Ext-atom5li0-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 7.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 7.2 MB