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- PDB-4z8c: Crystal structure of the Thermus thermophilus 70S ribosome bound ... -

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Basic information

Entry
Database: PDB / ID: 4z8c
TitleCrystal structure of the Thermus thermophilus 70S ribosome bound to translation inhibitor oncocin
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Initiator Methionine tRNA
  • Oncocin
  • mRNA
Keywordsribosome/antibiotic / Oncocin / antimicrobial peptide / antibiotic / 70S ribosome / inhibition of translation / peptidyl transferase inhibitors / 50S ribosomal subunit / peptide exit tunnel / ribosome-inhibitor complex / onc112 / ribosome-antibiotic complex
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase / 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 ...Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase / 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 L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L20 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / 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 S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / : / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / L28p-like / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...IRON/SULFUR CLUSTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / 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 / Alpha-N-acetylgalactosaminidase / 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 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 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)
Thermus thermophilus (bacteria)
Enterobacteria phage T4 (virus)
Oncopeltus fasciatus (milkweed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRoy, R.N. / Lomakin, I.B. / Gagnon, M.G. / Steitz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin.
Authors: Roy, R.N. / Lomakin, I.B. / Gagnon, M.G. / Steitz, T.A.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / entity_src_nat ...entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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
1v: mRNA
1x: Initiator Methionine tRNA
1z: Oncocin
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
2v: mRNA
2x: Initiator Methionine tRNA
2z: Oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,464,6012462
Polymers4,406,288110
Non-polymers58,3132352
Water71,8803990
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
1v: mRNA
1x: Initiator Methionine tRNA
1z: Oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,239,0821510
Polymers2,203,14455
Non-polymers35,9381455
Water81145
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
2v: mRNA
2x: Initiator Methionine tRNA
2z: Oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,225,520952
Polymers2,203,14455
Non-polymers22,376897
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.140, 450.730, 623.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11segid S031 or segid S071 or segid S091 or segid...
21segid S032 or segid S072 or segid S092 or segid...
12segid S021 or segid S041 or segid S051 or segid...
22segid S022 or segid S042 or segid S052 or segid...
13segid L091 and resid 41:146
23segid L092 and resid 41:146
14(segid L*1 and not ((segid L091 and resid 41:146) or...
24(segid L*2 and not ((segid L092 and resid 41:146) or...
15segid mRN1
25segid mRN2
16segid PtR1
26segid PtR2
17segid ONC1
27segid ONC2

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111segid S031 or segid S071 or segid S091 or segid...c2 - 5001
121segid S031 or segid S071 or segid S091 or segid...g2 - 156
131segid S031 or segid S071 or segid S091 or segid...i2 - 5001
141segid S031 or segid S071 or segid S091 or segid...j4 - 8001
151segid S031 or segid S071 or segid S091 or segid...m2 - 3002
161segid S031 or segid S071 or segid S091 or segid...n2 - 3002
171segid S031 or segid S071 or segid S091 or segid...s2 - 5001
181segid S031 or segid S071 or segid S091 or segid...u2 - 24
191segid S031 or segid S071 or segid S091 or segid...a5 - 8119
211segid S032 or segid S072 or segid S092 or segid...c2 - 5001
221segid S032 or segid S072 or segid S092 or segid...g2 - 156
231segid S032 or segid S072 or segid S092 or segid...i2 - 5002
241segid S032 or segid S072 or segid S092 or segid...j5 - 5001
251segid S032 or segid S072 or segid S092 or segid...m3 - 8001
261segid S032 or segid S072 or segid S092 or segid...n2 - 5002
271segid S032 or segid S072 or segid S092 or segid...s2 - 84
281segid S032 or segid S072 or segid S092 or segid...u2 - 24
291segid S032 or segid S072 or segid S092 or segid...a5 - 8112
112segid S021 or segid S041 or segid S051 or segid...b7 - 5002
122segid S021 or segid S041 or segid S051 or segid...d2 - 8002
132segid S021 or segid S041 or segid S051 or segid...e5 - 8002
142segid S021 or segid S041 or segid S051 or segid...f1 - 5001
152segid S021 or segid S041 or segid S051 or segid...h2 - 138
162segid S021 or segid S041 or segid S051 or segid...k13 - 3002
172segid S021 or segid S041 or segid S051 or segid...l5 - 3002
182segid S021 or segid S041 or segid S051 or segid...o2 - 5002
192segid S021 or segid S041 or segid S051 or segid...p1 - 82
1102segid S021 or segid S041 or segid S051 or segid...q2 - 3003
1112segid S021 or segid S041 or segid S051 or segid...r20 - 3002
1122segid S021 or segid S041 or segid S051 or segid...t8 - 3001
1132segid S021 or segid S041 or segid S051 or segid...a5 - 8119
212segid S022 or segid S042 or segid S052 or segid...b7 - 237
222segid S022 or segid S042 or segid S052 or segid...d2 - 3001
232segid S022 or segid S042 or segid S052 or segid...e5 - 5002
242segid S022 or segid S042 or segid S052 or segid...f1 - 3001
252segid S022 or segid S042 or segid S052 or segid...h2 - 5001
262segid S022 or segid S042 or segid S052 or segid...k13 - 8001
272segid S022 or segid S042 or segid S052 or segid...l5 - 8001
282segid S022 or segid S042 or segid S052 or segid...o2 - 5001
292segid S022 or segid S042 or segid S052 or segid...p1 - 5002
2102segid S022 or segid S042 or segid S052 or segid...q2 - 5002
2112segid S022 or segid S042 or segid S052 or segid...r20 - 5001
2122segid S022 or segid S042 or segid S052 or segid...t8 - 5002
2132segid S022 or segid S042 or segid S052 or segid...a5 - 8112
113segid L091 and resid 41:146I41 - 146
213segid L092 and resid 41:146I41 - 146
114(segid L*1 and not ((segid L091 and resid 41:146) or...D2 - 8006
124(segid L*1 and not ((segid L091 and resid 41:146) or...E1 - 8006
134(segid L*1 and not ((segid L091 and resid 41:146) or...F6 - 8002
144(segid L*1 and not ((segid L091 and resid 41:146) or...G2 - 8002
154(segid L*1 and not ((segid L091 and resid 41:146) or...H2 - 8002
164(segid L*1 and not ((segid L091 and resid 41:146) or...I1 - 146
174(segid L*1 and not ((segid L091 and resid 41:146) or...N1 - 8003
184(segid L*1 and not ((segid L091 and resid 41:146) or...O1 - 8001
194(segid L*1 and not ((segid L091 and resid 41:146) or...P1 - 8006
1104(segid L*1 and not ((segid L091 and resid 41:146) or...Q1 - 8002
1114(segid L*1 and not ((segid L091 and resid 41:146) or...R1 - 8004
1124(segid L*1 and not ((segid L091 and resid 41:146) or...S3 - 8001
1134(segid L*1 and not ((segid L091 and resid 41:146) or...T1 - 8005
1144(segid L*1 and not ((segid L091 and resid 41:146) or...U2 - 8001
1154(segid L*1 and not ((segid L091 and resid 41:146) or...V1 - 5001
1164(segid L*1 and not ((segid L091 and resid 41:146) or...W1 - 8001
1174(segid L*1 and not ((segid L091 and resid 41:146) or...X1 - 5002
1184(segid L*1 and not ((segid L091 and resid 41:146) or...Y1 - 3001
1194(segid L*1 and not ((segid L091 and resid 41:146) or...Z1 - 8002
1204(segid L*1 and not ((segid L091 and resid 41:146) or...010 - 8003
1214(segid L*1 and not ((segid L091 and resid 41:146) or...12 - 8002
1224(segid L*1 and not ((segid L091 and resid 41:146) or...21 - 5001
1234(segid L*1 and not ((segid L091 and resid 41:146) or...32 - 8002
1244(segid L*1 and not ((segid L091 and resid 41:146) or...41 - 501
1254(segid L*1 and not ((segid L091 and resid 41:146) or...52 - 8003
1264(segid L*1 and not ((segid L091 and resid 41:146) or...62 - 8002
1274(segid L*1 and not ((segid L091 and resid 41:146) or...71 - 5007
1284(segid L*1 and not ((segid L091 and resid 41:146) or...82 - 8002
1294(segid L*1 and not ((segid L091 and resid 41:146) or...91 - 8001
1304(segid L*1 and not ((segid L091 and resid 41:146) or...A5 - 8670
1314(segid L*1 and not ((segid L091 and resid 41:146) or...B1 - 8013
214(segid L*2 and not ((segid L092 and resid 41:146) or...D2 - 5010
224(segid L*2 and not ((segid L092 and resid 41:146) or...E1 - 8003
234(segid L*2 and not ((segid L092 and resid 41:146) or...F6 - 8001
244(segid L*2 and not ((segid L092 and resid 41:146) or...G2 - 3001
254(segid L*2 and not ((segid L092 and resid 41:146) or...H2 - 175
264(segid L*2 and not ((segid L092 and resid 41:146) or...I1 - 146
274(segid L*2 and not ((segid L092 and resid 41:146) or...N1 - 8001
284(segid L*2 and not ((segid L092 and resid 41:146) or...O1 - 8002
294(segid L*2 and not ((segid L092 and resid 41:146) or...P1 - 5001
2104(segid L*2 and not ((segid L092 and resid 41:146) or...Q1 - 5002
2114(segid L*2 and not ((segid L092 and resid 41:146) or...R1 - 5001
2124(segid L*2 and not ((segid L092 and resid 41:146) or...S3 - 112
2134(segid L*2 and not ((segid L092 and resid 41:146) or...T1 - 8001
2144(segid L*2 and not ((segid L092 and resid 41:146) or...U2 - 5002
2154(segid L*2 and not ((segid L092 and resid 41:146) or...V1 - 5001
2164(segid L*2 and not ((segid L092 and resid 41:146) or...W1 - 5001
2174(segid L*2 and not ((segid L092 and resid 41:146) or...X1 - 8001
2184(segid L*2 and not ((segid L092 and resid 41:146) or...Y1 - 8001
2194(segid L*2 and not ((segid L092 and resid 41:146) or...Z1 - 5001
2204(segid L*2 and not ((segid L092 and resid 41:146) or...010 - 8001
2214(segid L*2 and not ((segid L092 and resid 41:146) or...12 - 98
2224(segid L*2 and not ((segid L092 and resid 41:146) or...21 - 70
2234(segid L*2 and not ((segid L092 and resid 41:146) or...32 - 60
2244(segid L*2 and not ((segid L092 and resid 41:146) or...41 - 501
2254(segid L*2 and not ((segid L092 and resid 41:146) or...52 - 5001
2264(segid L*2 and not ((segid L092 and resid 41:146) or...62 - 501
2274(segid L*2 and not ((segid L092 and resid 41:146) or...71 - 48
2284(segid L*2 and not ((segid L092 and resid 41:146) or...82 - 8001
2294(segid L*2 and not ((segid L092 and resid 41:146) or...91 - 501
2304(segid L*2 and not ((segid L092 and resid 41:146) or...A5 - 8316
2314(segid L*2 and not ((segid L092 and resid 41:146) or...B1 - 8004
115segid mRN1v14 - 18
215segid mRN2v14 - 18
116segid PtR1x2 - 8003
216segid PtR2x2 - 8001
117segid ONC1z1 - 8001
217segid ONC2z1 - 5001

NCS ensembles :
ID
1
2
3
4
5
6
7

-
Components

-
RNA chain , 5 types, 10 molecules 1A2A1B2B1a2a1v2v1x2x

#1: RNA chain 23S ribosomal RNA


Mass: 947895.375 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: 55771382
#32: RNA chain 16S ribosomal RNA


Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#53: RNA chain mRNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Enterobacteria phage T4 (virus)
#54: RNA chain Initiator Methionine tRNA


Mass: 24846.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 732678099

+
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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

-
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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#43: Protein 30S ribosomal protein S12


Mass: 14637.384 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
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Protein/peptide , 1 types, 2 molecules 1z2z

#55: Protein/peptide Oncocin


Mass: 2396.837 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: GenScript-Synthesized 19-amino acid peptide oncocin
Source: (synth.) Oncopeltus fasciatus (milkweed bug)

-
Non-polymers , 4 types, 6342 molecules

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


Mass: 24.305 Da / Num. of mol.: 2338 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 3990 / 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: 3.35 Å3/Da / Density % sol: 58.37 % / 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, 2.9% PEG-20K, 7-12% MPD, 0.5 mM BME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2014 / Details: S/N 60-0112-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. all: 1433648 / Num. obs: 1407992 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.848 % / Biso Wilson estimate: 61.23 Å2 / Rmerge F obs: 0.993 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.213 / Χ2: 0.939 / Net I/σ(I): 7.03 / Num. measured all: 5417877
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.1742.1120.66348707105609992632.46694
2.87-2.950.2731.5390.964055271027871025731.77299.8
2.95-3.040.4071.1321.31391777100045998191.30499.8
3.04-3.130.5660.8161.8237760797300966910.94199.4
3.13-3.230.6970.6132.436153194252937990.70899.5
3.23-3.350.7840.4833.0134295991108906760.55999.5
3.35-3.470.8330.4013.4630576388036866930.46998.5
3.47-3.610.8930.3244.432776084848843820.37399.5
3.61-3.780.9330.2545.5532086781265808660.29199.5
3.78-3.960.9560.2016.8330465977869773320.23199.3
3.96-4.170.9690.1648.0928587774045729080.18998.5
4.17-4.430.9780.1339.5526203970077688970.15498.3
4.43-4.730.9840.10811.1423592365959645870.12697.9
4.73-5.110.9880.09413.2924524361483605520.10898.5
5.11-5.60.9910.08115.122201656574553060.09397.8
5.6-6.260.9920.07615.7519558351420495200.08796.3
6.26-7.230.9930.0651716034245412433610.07695.5
7.23-8.850.9950.05322.0615197438517370800.06196.3
8.85-12.520.9970.0427.9411147930076282710.04794
12.52-600.9970.03235.86024416966154160.03790.9

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→59.981 Å / FOM work R set: 0.8194 / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 63740 5.01 %
Rwork0.2029 1208169 -
obs0.2051 1271909 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.98 Å2 / Biso mean: 59.85 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 2.9→59.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90537 191485 5155 1201 288378
Biso mean--49.81 41.99 -
Num. residues----20530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004310301
X-RAY DIFFRACTIONf_angle_d0.717461532
X-RAY DIFFRACTIONf_chiral_restr0.03258233
X-RAY DIFFRACTIONf_plane_restr0.00424974
X-RAY DIFFRACTIONf_dihedral_angle_d15.108142285
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDRmsType
116922X-RAY DIFFRACTION13.983TORSIONAL
126922X-RAY DIFFRACTION13.983TORSIONAL
2112769X-RAY DIFFRACTION13.983TORSIONAL
2212769X-RAY DIFFRACTION13.983TORSIONAL
31824X-RAY DIFFRACTION13.983TORSIONAL
32824X-RAY DIFFRACTION13.983TORSIONAL
4132682X-RAY DIFFRACTION13.983TORSIONAL
4232682X-RAY DIFFRACTION13.983TORSIONAL
51114X-RAY DIFFRACTION13.983TORSIONAL
52114X-RAY DIFFRACTION13.983TORSIONAL
611724X-RAY DIFFRACTION13.983TORSIONAL
621724X-RAY DIFFRACTION13.983TORSIONAL
71140X-RAY DIFFRACTION13.983TORSIONAL
72140X-RAY DIFFRACTION13.983TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.9330.371321600.33714047242632100
2.933-2.96750.366321360.32424061042746100
2.9675-3.00360.359321180.31154063242750100
3.0036-3.04170.351721610.30044042942590100
3.0417-3.08170.339820990.2884403644246399
3.0817-3.12390.337621560.2856404264258299
3.1239-3.16850.318420930.27094060042693100
3.1685-3.21580.313821450.26064045242597100
3.2158-3.26610.303121020.2514053842640100
3.2661-3.31960.308921120.24614059742709100
3.3196-3.37680.288820770.2344402354231299
3.3768-3.43820.297821160.2368402484236499
3.4382-3.50440.284421220.2298401364225898
3.5044-3.57590.274321880.22144051242700100
3.5759-3.65360.272121030.21394059542698100
3.6536-3.73860.253221390.20044057442713100
3.7386-3.83210.242221690.1956405294269899
3.8321-3.93570.237920560.1897405454260199
3.9357-4.05150.234621440.1862402764242099
4.0515-4.18220.225421650.1826402194238498
4.1822-4.33160.223521140.1792402164233098
4.3316-4.5050.232221360.18399974213398
4.505-4.710.211721310.1691400444217598
4.71-4.95820.213421490.1664404024255199
4.9582-5.26870.209321150.1622403164243198
5.2687-5.67520.204921280.1566400444217298
5.6752-6.24570.202421390.1617394544159396
6.2457-7.14830.209420520.1687394394149195
7.1483-9.00120.202121730.1739398784205196
9.0012-59.99380.221320420.2028393904143293

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