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- PDB-7azo: 70S thermus thermophilus ribosome with bound antibiotic lead SEQ-977 -

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Basic information

Entry
Database: PDB / ID: 7azo
Title70S thermus thermophilus ribosome with bound antibiotic lead SEQ-977
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • (Phe-tRNA) x 5
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • RNA (30-MER)
KeywordsRIBOSOME / translation / RNA / antibiotics
Function / homology
Function and homology information


large ribosomal subunit / 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 ...large ribosomal subunit / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein
Similarity search - Domain/homology
: / osmium (III) hexammine / Chem-SJE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 ...: / osmium (III) hexammine / Chem-SJE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Thermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJenner, L.B. / Yusupov, M. / Yusupova, G.
CitationJournal: Cell / Year: 2023
Title: Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents.
Authors: Jidong Zhang / Christine Lair / Christine Roubert / Kwame Amaning / María Belén Barrio / Yannick Benedetti / Zhicheng Cui / Zhongliang Xing / Xiaojun Li / Scott G Franzblau / Nicolas ...Authors: Jidong Zhang / Christine Lair / Christine Roubert / Kwame Amaning / María Belén Barrio / Yannick Benedetti / Zhicheng Cui / Zhongliang Xing / Xiaojun Li / Scott G Franzblau / Nicolas Baurin / Florence Bordon-Pallier / Cathy Cantalloube / Stephanie Sans / Sandra Silve / Isabelle Blanc / Laurent Fraisse / Alexey Rak / Lasse B Jenner / Gulnara Yusupova / Marat Yusupov / Junjie Zhang / Takushi Kaneko / T J Yang / Nader Fotouhi / Eric Nuermberger / Sandeep Tyagi / Fabrice Betoudji / Anna Upton / James C Sacchettini / Sophie Lagrange /
Abstract: The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding ...The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.
History
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
16SA: 16S rRNA
S2A: 30S ribosomal protein S2
S3A: 30S ribosomal protein S3
S4A: 30S ribosomal protein S4
S5A: 30S ribosomal protein S5
S6A: 30S ribosomal protein S6
S7A: 30S ribosomal protein S7
S8A: 30S ribosomal protein S8
S9A: 30S ribosomal protein S9
S10A: 30S ribosomal protein S10
S11A: 30S ribosomal protein S11
S12A: 30S ribosomal protein S12
S13A: 30S ribosomal protein S13
S14A: 30S ribosomal protein S14 type Z
S15A: 30S ribosomal protein S15
S16A: 30S ribosomal protein S16
S17A: 30S ribosomal protein S17
S18A: 30S ribosomal protein S18
S19A: 30S ribosomal protein S19
S20A: 30S ribosomal protein S20
THXA: 30S ribosomal protein Thx
ASIA: Phe-tRNA
PSIA: Phe-tRNA
ESIA: Phe-tRNA
MRNA: RNA (30-MER)
TRNA: Phe-tRNA
23SA: 23S rRNA
5SA: 5S rRNA
L2A: 50S ribosomal protein L2
L3A: 50S ribosomal protein L3
L4A: 50S ribosomal protein L4
L5A: 50S ribosomal protein L5
L6A: 50S ribosomal protein L6
L9A: 50S ribosomal protein L9
L13A: 50S ribosomal protein L13
L14A: 50S ribosomal protein L14
L15A: 50S ribosomal protein L15
L16A: 50S ribosomal protein L16
L17A: 50S ribosomal protein L17
L18A: 50S ribosomal protein L18
L19A: 50S ribosomal protein L19
L20A: 50S ribosomal protein L20
L21A: 50S ribosomal protein L21
L22A: 50S ribosomal protein L22
L23A: 50S ribosomal protein L23
L24A: 50S ribosomal protein L24
L25A: 50S ribosomal protein L25
L27A: 50S ribosomal protein L27
L28A: 50S ribosomal protein L28
L29A: 50S ribosomal protein L29
L30A: 50S ribosomal protein L30
L31A: 50S ribosomal protein L31
L32A: 50S ribosomal protein L32
L33A: 50S ribosomal protein L33
L34A: 50S ribosomal protein L34
L35A: 50S ribosomal protein L35
16SB: 16S rRNA
S2B: 30S ribosomal protein S2
S3B: 30S ribosomal protein S3
S4B: 30S ribosomal protein S4
S5B: 30S ribosomal protein S5
S6B: 30S ribosomal protein S6
S7B: 30S ribosomal protein S7
S8B: 30S ribosomal protein S8
S9B: 30S ribosomal protein S9
S10B: 30S ribosomal protein S10
S11B: 30S ribosomal protein S11
S12B: 30S ribosomal protein S12
S13B: 30S ribosomal protein S13
S14B: 30S ribosomal protein S14 type Z
S15B: 30S ribosomal protein S15
S16B: 30S ribosomal protein S16
S17B: 30S ribosomal protein S17
S18B: 30S ribosomal protein S18
S19B: 30S ribosomal protein S19
S20B: 30S ribosomal protein S20
THXB: 30S ribosomal protein Thx
ASIB: Phe-tRNA
PSIB: Phe-tRNA
ESIB: Phe-tRNA
MRNB: RNA (30-MER)
23SB: 23S rRNA
5SB: 5S rRNA
L2B: 50S ribosomal protein L2
L3B: 50S ribosomal protein L3
L4B: 50S ribosomal protein L4
L5B: 50S ribosomal protein L5
L6B: 50S ribosomal protein L6
L9B: 50S ribosomal protein L9
L13B: 50S ribosomal protein L13
L14B: 50S ribosomal protein L14
L15B: 50S ribosomal protein L15
L16B: 50S ribosomal protein L16
L17B: 50S ribosomal protein L17
L18B: 50S ribosomal protein L18
L19B: 50S ribosomal protein L19
L20B: 50S ribosomal protein L20
L21B: 50S ribosomal protein L21
L22B: 50S ribosomal protein L22
L23B: 50S ribosomal protein L23
L24B: 50S ribosomal protein L24
L25B: 50S ribosomal protein L25
L27B: 50S ribosomal protein L27
L28B: 50S ribosomal protein L28
L29B: 50S ribosomal protein L29
L30B: 50S ribosomal protein L30
L31B: 50S ribosomal protein L31
L32B: 50S ribosomal protein L32
L33B: 50S ribosomal protein L33
L34B: 50S ribosomal protein L34
L35B: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,723,5841807
Polymers4,513,420111
Non-polymers210,1641696
Water31,7781764
1
16SA: 16S rRNA
S2A: 30S ribosomal protein S2
S3A: 30S ribosomal protein S3
S4A: 30S ribosomal protein S4
S5A: 30S ribosomal protein S5
S6A: 30S ribosomal protein S6
S7A: 30S ribosomal protein S7
S8A: 30S ribosomal protein S8
S9A: 30S ribosomal protein S9
S10A: 30S ribosomal protein S10
S11A: 30S ribosomal protein S11
S12A: 30S ribosomal protein S12
S13A: 30S ribosomal protein S13
S14A: 30S ribosomal protein S14 type Z
S15A: 30S ribosomal protein S15
S16A: 30S ribosomal protein S16
S17A: 30S ribosomal protein S17
S18A: 30S ribosomal protein S18
S19A: 30S ribosomal protein S19
S20A: 30S ribosomal protein S20
THXA: 30S ribosomal protein Thx
ASIA: Phe-tRNA
PSIA: Phe-tRNA
ESIA: Phe-tRNA
MRNA: RNA (30-MER)
TRNA: Phe-tRNA
23SA: 23S rRNA
5SA: 5S rRNA
L2A: 50S ribosomal protein L2
L3A: 50S ribosomal protein L3
L4A: 50S ribosomal protein L4
L5A: 50S ribosomal protein L5
L6A: 50S ribosomal protein L6
L9A: 50S ribosomal protein L9
L13A: 50S ribosomal protein L13
L14A: 50S ribosomal protein L14
L15A: 50S ribosomal protein L15
L16A: 50S ribosomal protein L16
L17A: 50S ribosomal protein L17
L18A: 50S ribosomal protein L18
L19A: 50S ribosomal protein L19
L20A: 50S ribosomal protein L20
L21A: 50S ribosomal protein L21
L22A: 50S ribosomal protein L22
L23A: 50S ribosomal protein L23
L24A: 50S ribosomal protein L24
L25A: 50S ribosomal protein L25
L27A: 50S ribosomal protein L27
L28A: 50S ribosomal protein L28
L29A: 50S ribosomal protein L29
L30A: 50S ribosomal protein L30
L31A: 50S ribosomal protein L31
L32A: 50S ribosomal protein L32
L33A: 50S ribosomal protein L33
L34A: 50S ribosomal protein L34
L35A: 50S ribosomal protein L35
hetero molecules


  • defined by author
  • 2.38 MDa, 56 polymers
Theoretical massNumber of molelcules
Total (without water)2,378,477982
Polymers2,269,04256
Non-polymers109,435926
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
16SB: 16S rRNA
S2B: 30S ribosomal protein S2
S3B: 30S ribosomal protein S3
S4B: 30S ribosomal protein S4
S5B: 30S ribosomal protein S5
S6B: 30S ribosomal protein S6
S7B: 30S ribosomal protein S7
S8B: 30S ribosomal protein S8
S9B: 30S ribosomal protein S9
S10B: 30S ribosomal protein S10
S11B: 30S ribosomal protein S11
S12B: 30S ribosomal protein S12
S13B: 30S ribosomal protein S13
S14B: 30S ribosomal protein S14 type Z
S15B: 30S ribosomal protein S15
S16B: 30S ribosomal protein S16
S17B: 30S ribosomal protein S17
S18B: 30S ribosomal protein S18
S19B: 30S ribosomal protein S19
S20B: 30S ribosomal protein S20
THXB: 30S ribosomal protein Thx
ASIB: Phe-tRNA
PSIB: Phe-tRNA
ESIB: Phe-tRNA
MRNB: RNA (30-MER)
23SB: 23S rRNA
5SB: 5S rRNA
L2B: 50S ribosomal protein L2
L3B: 50S ribosomal protein L3
L4B: 50S ribosomal protein L4
L5B: 50S ribosomal protein L5
L6B: 50S ribosomal protein L6
L9B: 50S ribosomal protein L9
L13B: 50S ribosomal protein L13
L14B: 50S ribosomal protein L14
L15B: 50S ribosomal protein L15
L16B: 50S ribosomal protein L16
L17B: 50S ribosomal protein L17
L18B: 50S ribosomal protein L18
L19B: 50S ribosomal protein L19
L20B: 50S ribosomal protein L20
L21B: 50S ribosomal protein L21
L22B: 50S ribosomal protein L22
L23B: 50S ribosomal protein L23
L24B: 50S ribosomal protein L24
L25B: 50S ribosomal protein L25
L27B: 50S ribosomal protein L27
L28B: 50S ribosomal protein L28
L29B: 50S ribosomal protein L29
L30B: 50S ribosomal protein L30
L31B: 50S ribosomal protein L31
L32B: 50S ribosomal protein L32
L33B: 50S ribosomal protein L33
L34B: 50S ribosomal protein L34
L35B: 50S ribosomal protein L35
hetero molecules


  • defined by author
  • 2.35 MDa, 55 polymers
Theoretical massNumber of molelcules
Total (without water)2,345,107825
Polymers2,244,37755
Non-polymers100,730770
Water30617
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.770, 446.870, 616.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain , 9 types, 15 molecules 16SA16SBASIAPSIAPSIBESIAESIBMRNAMRNBTRNA23SA23SB5SA5SBASIB

#1: RNA chain 16S rRNA


Mass: 491070.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#22: RNA chain Phe-tRNA


Mass: 24644.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1850831943
#23: RNA chain Phe-tRNA


Mass: 24747.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#24: RNA chain Phe-tRNA


Mass: 24599.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#25: RNA chain RNA (30-MER)


Mass: 9442.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria)
#26: RNA chain Phe-tRNA


Mass: 24633.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1850831943
#27: RNA chain 23S rRNA


Mass: 946779.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#28: RNA chain 5S rRNA


Mass: 40152.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#57: RNA chain Phe-tRNA


Mass: 24613.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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30S ribosomal protein ... , 20 types, 40 molecules S2AS2BS3AS3BS4AS4BS5AS5BS6AS6BS7AS7BS8AS8BS9AS9BS10AS10BS11AS11BS12AS12BS13AS13BS14AS14BS15AS15BS16AS16B...

#2: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9
#9: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6
#15: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY7
#18: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

+
50S ribosomal protein ... , 28 types, 56 molecules L2AL2BL3AL3BL4AL4BL5AL5BL6AL6BL9AL9BL13AL13BL14AL14BL15AL15BL16AL16BL17AL17BL18AL18BL19AL19BL20AL20BL21AL21B...

#29: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#30: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#31: Protein 50S ribosomal protein L4 / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#32: Protein 50S ribosomal protein L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#33: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY8
#34: Protein 50S ribosomal protein L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#35: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#36: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#37: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#38: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#39: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#40: Protein 50S ribosomal protein L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#41: Protein 50S ribosomal protein L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#42: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#43: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#44: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#45: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#46: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#47: Protein 50S ribosomal protein L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#48: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#49: Protein 50S ribosomal protein L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#50: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#51: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#52: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#53: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#54: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#55: Protein/peptide 50S ribosomal protein L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#56: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1

-
Non-polymers , 5 types, 3460 molecules

#58: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 788 / Source method: obtained synthetically / Formula: Mg
#59: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 619 / Source method: obtained synthetically / Formula: H12N6Os
#60: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 287 / Source method: obtained synthetically / Formula: K
#61: Chemical ChemComp-SJE / (2R,3S,4R,5R,7S,9S,10S,11R,12S,13R)-12-(((2R,4R,5S,6S)-4,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl)oxy)-2-((S)-1-(((2R,3R,4R,5R,6R)-5-hydroxy-3,4-dimethoxy-6-methyltetrahydro-2H-pyran-2-yl)oxy)propan-2-yl)-10-(((2S,3R,4R,6R)-3-hydroxy-4-(methoxyamino)-6-methyltetrahydro-2H-pyran-2-yl)oxy)-3,5,7,9,11,13-hexamethyl-7-(((2-((2-nitrophenyl)sulfonamido)ethyl)carbamoyl)oxy)-6,14-dioxooxacyclotetradecan-4-yl 3-methylbutanoate / [(2~{R},3~{S},4~{R},5~{R},7~{S},9~{S},10~{S},11~{R},12~{S},13~{R})-2-[(2~{S})-1-[(2~{R},3~{R},4~{R},5~{R},6~{R})-3,4-dimethoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxypropan-2-yl]-12-[(2~{R},4~{R},5~{S},6~{S})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-10-[(2~{S},3~{R},4~{R},6~{R})-4-(methoxyamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-3,5,7,9,11,13-hexamethyl-7-[2-[(2-nitrophenyl)sulfonylamino]ethylcarbamoyloxy]-6,14-bis(oxidanylidene)-1-oxacyclotetradec-4-yl] 3-methylbutanoate


Mass: 1265.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C58H96N4O24S
#62: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1764 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG2000MMES, KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→300 Å / Num. obs: 860556 / % possible obs: 100 % / Redundancy: 30 % / Biso Wilson estimate: 93.11 Å2 / Rrim(I) all: 0.42 / Net I/σ(I): 9.72
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 73202 / Rrim(I) all: 3.13

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V6F

4v6f


Resolution: 3.3→253.87 Å / SU ML: 0.4118 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.9236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 25660 2.98 %
Rwork0.2143 834848 -
obs0.215 860508 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.58 Å2
Refinement stepCycle: LAST / Resolution: 3.3→253.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms92208 206848 7346 0 306402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052330972
X-RAY DIFFRACTIONf_angle_d1.1607500566
X-RAY DIFFRACTIONf_chiral_restr0.056461798
X-RAY DIFFRACTIONf_plane_restr0.007625834
X-RAY DIFFRACTIONf_dihedral_angle_d17.7497152039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.340.3368450.309827691X-RAY DIFFRACTION99.93
3.34-3.380.32998750.298127589X-RAY DIFFRACTION100
3.38-3.420.31719030.28727559X-RAY DIFFRACTION100
3.42-3.460.31028310.281327663X-RAY DIFFRACTION100
3.46-3.510.30348470.276827775X-RAY DIFFRACTION100
3.51-3.550.31158870.270127582X-RAY DIFFRACTION100
3.55-3.610.29558790.258527662X-RAY DIFFRACTION100
3.61-3.660.28128350.249127662X-RAY DIFFRACTION100
3.66-3.720.26658080.243627710X-RAY DIFFRACTION99.99
3.72-3.780.27648210.24127667X-RAY DIFFRACTION100
3.78-3.840.27628200.24127746X-RAY DIFFRACTION100
3.84-3.910.25078290.226527739X-RAY DIFFRACTION100
3.91-3.990.23838870.215627716X-RAY DIFFRACTION100
3.99-4.070.23948990.212927625X-RAY DIFFRACTION99.99
4.07-4.160.24168460.207827757X-RAY DIFFRACTION99.99
4.16-4.250.24288120.205227834X-RAY DIFFRACTION100
4.25-4.360.23388890.201627725X-RAY DIFFRACTION99.99
4.36-4.480.22678870.200827692X-RAY DIFFRACTION100
4.48-4.610.21448320.199527813X-RAY DIFFRACTION100
4.61-4.760.22638570.203527823X-RAY DIFFRACTION100
4.76-4.930.22768560.195627743X-RAY DIFFRACTION100
4.93-5.130.22498110.189727952X-RAY DIFFRACTION100
5.13-5.360.20938450.183227862X-RAY DIFFRACTION100
5.36-5.640.218490.182527898X-RAY DIFFRACTION100
5.64-60.20728910.187127912X-RAY DIFFRACTION100
6-6.460.21358870.192427890X-RAY DIFFRACTION100
6.46-7.110.21898150.19728119X-RAY DIFFRACTION100
7.11-8.140.22437970.201428214X-RAY DIFFRACTION99.99
8.14-10.250.23249150.215228234X-RAY DIFFRACTION99.99
10.25-253.870.20779050.210228994X-RAY DIFFRACTION99.87

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