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- PDB-8fc5: Crystal structure of the A2058-N6-dimethylated Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 8fc5
TitleCrystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.65A resolution
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Ribosome-associated inhibitor A
KeywordsRIBOSOME / Hygromycin A / macrolides / ketolides / erythromycin / azithromycin / telithromycin / antibiotic / synergy / Erm methyltransferase / X-ray structure / 70S ribosome / peptidyl transferase center / nascent peptide exit tunnel
Function / homology
Function and homology information


dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity ...dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 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 ...: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 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 L36 signature. / 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein L20 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / 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 L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / 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 L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein
Similarity search - Domain/homology
ARGININE / Hygromycin A / IRON/SULFUR CLUSTER / AZITHROMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...ARGININE / Hygromycin A / IRON/SULFUR CLUSTER / AZITHROMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome-associated inhibitor A / 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 bL36 / 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 speciesEscherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChen, C.-W. / Syroegin, E.A. / Svetlov, M.S. / Polikanov, Y.S.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM132302 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI162961 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI152210 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI173064 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI137584 United States
Other governmentUniversity of Illinois Startup Funds
Other privateSteven and Alexandra Cohen Foundation
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A.
Authors: Chen, C.W. / Leimer, N. / Syroegin, E.A. / Dunand, C. / Bulman, Z.P. / Lewis, K. / Polikanov, Y.S. / Svetlov, M.S.
History
DepositionDec 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1y: Ribosome-associated inhibitor A
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2y: Ribosome-associated inhibitor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,427,7172599
Polymers4,362,594106
Non-polymers65,1232493
Water139,6167750
1
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1y: Ribosome-associated inhibitor A
hetero molecules


  • defined by author
  • 2.22 MDa, 53 polymers
Theoretical massNumber of molelcules
Total (without water)2,220,5821568
Polymers2,181,29753
Non-polymers39,2851515
Water75742
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2y: Ribosome-associated inhibitor A
hetero molecules


  • defined by author
  • 2.21 MDa, 53 polymers
Theoretical massNumber of molelcules
Total (without water)2,207,1351031
Polymers2,181,29753
Non-polymers25,838978
Water75742
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.550, 449.770, 619.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 3 types, 6 molecules 1A2A1B2B1a2a

#1: RNA chain 23S Ribosomal RNA


Mass: 948035.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S Ribosomal RNA


Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: AP008226.1
#32: RNA chain 16S Ribosomal RNA


Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382

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50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...

#3: Protein 50S ribosomal protein L2


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


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN8
#5: 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 HB8 (bacteria) / References: UniProt: Q5SHN9
#6: Protein 50S ribosomal protein L5


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


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


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


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


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


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


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


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9Z9H5
#14: 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 HB8 (bacteria) / References: UniProt: Q5SHQ4
#15: Protein 50S ribosomal protein L19


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


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


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


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


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


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP9
#21: 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 HB8 (bacteria) / References: UniProt: Q5SHZ1
#22: Protein 50S ribosomal protein L27


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


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


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


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


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


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


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P35871
#29: 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 HB8 (bacteria) / References: UniProt: P80340
#30: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SKU1
#31: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHR2

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30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...

#33: Protein 30S ribosomal protein S2


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


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


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


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#37: 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 HB8 (bacteria) / References: UniProt: Q5SLP8
#38: Protein 30S ribosomal protein S7


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


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


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


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


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


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


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#45: 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 HB8 (bacteria) / References: UniProt: P0DOY6
#46: Protein 30S ribosomal protein S15


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


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


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


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


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


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#52: 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 HB8 (bacteria) / References: UniProt: Q5SIH3

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Protein , 1 types, 2 molecules 1y2y

#53: Protein Ribosome-associated inhibitor A / Protein Y / pY / Ribosome associated factor Y / Spot Y


Mass: 12803.583 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: raiA, yfiA, b2597, JW2578 / Plasmid: pGS21a-YFIA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AD49

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Non-polymers , 8 types, 10243 molecules

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


Mass: 24.305 Da / Num. of mol.: 2466 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-HGR / Hygromycin A


Mass: 511.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29NO12 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#56: Chemical ChemComp-ZIT / AZITHROMYCIN


Mass: 748.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H72N2O12 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#57: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#58: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7750 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.31 % / Description: Long needles
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 26, 2022 / Details: S/N E-32-0124
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→153.31 Å / Num. obs: 1668125 / % possible obs: 99.8 % / Redundancy: 6.836 % / Biso Wilson estimate: 63.032 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.22 / Χ2: 1.064 / Net I/σ(I): 8.1 / Num. measured all: 11403235 / Scaling rejects: 9755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.726.9782.1480.988574941230741228900.2642.3299.9
2.72-2.796.8831.7371.218255421199631199330.3561.879100
2.79-2.876.7261.3451.557838451165761165460.4761.459100
2.87-2.966.2120.9712.037017241132491129680.581.06199.8
2.96-3.066.90.7352.937574151098901097740.7590.79499.9
3.06-3.177.2270.5474.127679721062911062590.8660.589100
3.17-3.297.2160.4325.37398161026431025270.9110.46699.9
3.29-3.427.1190.3566.4370277498788987170.9370.38499.9
3.42-3.577.0280.3037.5166555094801947030.9510.32799.9
3.57-3.756.9020.258.9662534190710906050.9650.27199.9
3.75-3.956.7180.20710.5257856686258861230.9740.22499.8
3.95-4.196.4320.17611.852412181693814890.9780.19199.8
4.19-4.485.9760.14712.9845667076853764110.9830.16199.4
4.48-4.846.9870.1315.5349991171586715480.9890.14199.9
4.84-5.37.0120.1131746255165998659640.9920.12399.9
5.3-5.937.0380.118.0642065459810597690.9930.10999.9
5.93-6.847.0010.0918.4136995452882528440.9940.09799.9
6.84-8.386.410.07319.8828651744910446980.9940.0899.5
8.38-11.856.9450.0623.6224158834963347860.9960.06599.5
11.85-153.316.910.05226.3813523019744195710.9920.05799.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.8.2model building
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XHX

6xhx


Resolution: 2.65→153.31 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 83715 5.02 %
Rwork0.1944 1584173 -
obs0.1965 1667888 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.55 Å2 / Biso mean: 62.9942 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 2.65→153.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms93012 193352 2750 7755 296869
Biso mean--57.4 48.12 -
Num. residues----20814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004315568
X-RAY DIFFRACTIONf_angle_d0.873471290
X-RAY DIFFRACTIONf_chiral_restr0.04258972
X-RAY DIFFRACTIONf_plane_restr0.00525448
X-RAY DIFFRACTIONf_dihedral_angle_d16.309144856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.680.367927850.33735253855323100
2.68-2.710.358227830.31995248055263100
2.71-2.740.360227190.3155259455313100
2.74-2.780.350928060.30745257955385100
2.78-2.820.34927960.30125260455400100
2.82-2.850.33728670.28635252055387100
2.85-2.90.319727830.27475269255475100
2.9-2.940.315428180.26775262955447100
2.94-2.980.305327410.2648522975503899
2.98-3.030.305927940.26015265855452100
3.03-3.090.301327400.24545275355493100
3.09-3.140.275127570.22275271855475100
3.14-3.20.266627800.21315261555395100
3.2-3.270.249427410.20545280155542100
3.27-3.340.249627550.19975267755432100
3.34-3.420.245727350.19655275055485100
3.42-3.50.240827900.19575274455534100
3.5-3.60.240727870.19235278855575100
3.6-3.70.235627980.18455270355501100
3.7-3.820.225227840.17995283255616100
3.82-3.960.222727170.17535282355540100
3.96-4.120.21728230.17515276255585100
4.12-4.30.21427910.17375268955480100
4.3-4.530.214727960.17025273455530100
4.53-4.820.208428350.16615296655801100
4.82-5.190.199528080.15915308055888100
5.19-5.710.200828420.15575316456006100
5.71-6.540.205628530.16245332756180100
6.54-8.230.202828160.16545343856254100
8.23-153.310.199528750.185542185709399

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