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- PDB-6n9f: Crystal structure of the Thermus thermophilus 70S ribosome in com... -

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Basic information

Entry
Database: PDB / ID: 6n9f
TitleCrystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic ACCA-DPhe and bound to mRNA and P-site tRNA at 3.7A resolution
Components
  • (30S Ribosomal Protein ...) x 20
  • (50S Ribosomal Protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • ACCA-DPhe
  • P-site tRNA, Deacylated Initiator Methionyl-tRNA
  • mRNA
KeywordsRIBOSOME / D-amino acids / ribosome structure / peptidyl transferase center / expanded genetic code / ribosome engineering
Function / homology
Function and homology information


large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome ...large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / 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 ...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 L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28 / Ribosomal protein S13, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S11, bacterial-type / Ribosomal protein L5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal L32p protein family / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein L24 / Ribosomal protein S18 superfamily / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein S10 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S15 signature. / Ribosomal protein S10p/S20e / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein L24 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein L24/L26, conserved site / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 ...IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsMelnikov, S.V. / Khabibullina, N.F. / Mairhofer, E. / Vargas-Rodriguez, O. / Reynolds, N.M. / Micura, R. / Soll, D. / Polikanov, Y.S.
Funding support United States, Austria, 3items
OrganizationGrant numberCountry
Illinois State Startup Funds United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-GM122560 United States
Austrian Science FundP27947 Austria
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.
Authors: Melnikov, S.V. / Khabibullina, N.F. / Mairhofer, E. / Vargas-Rodriguez, O. / Reynolds, N.M. / Micura, R. / Soll, D. / Polikanov, Y.S.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_PDB_ins_code / _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.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_PDB_ins_code / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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.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_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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
Revision 1.8Mar 19, 2025Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _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

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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
1w: ACCA-DPhe
1x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
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
2w: ACCA-DPhe
2x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,439,0651463
Polymers4,405,032110
Non-polymers34,0331353
Water4,450247
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
1w: ACCA-DPhe
1x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,220,517772
Polymers2,202,51655
Non-polymers18,001717
Water1448
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
2w: ACCA-DPhe
2x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,218,548691
Polymers2,202,51655
Non-polymers16,032636
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.390, 452.150, 617.640
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 , 6 types, 12 molecules 1A2A1B2B1a2a1v2v1w2w1x2x

#1: RNA chain 23S Ribosomal RNA


Mass: 948035.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#32: RNA chain 16S Ribosomal RNA


Mass: 493864.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#53: RNA chain mRNA


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


Mass: 1370.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic tRNA-mimic ACCA-DPhe / Source: (synth.) Escherichia coli (E. coli)
#55: RNA chain P-site tRNA, Deacylated Initiator Methionyl-tRNA


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

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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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#5: Protein 50S Ribosomal Protein L4


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#14: Protein 50S Ribosomal Protein L18


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8 / References: UniProt: Q56435
#21: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q72IA7
#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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: Q72I12
#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 (bacteria) / Strain: HB8 / References: UniProt: P74909
#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 (bacteria) / Strain: HB8 / References: UniProt: Q72JR0
#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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: Q72GW3
#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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8
#31: Protein/peptide 50S Ribosomal Protein L36


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

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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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#37: Protein 30S Ribosomal Protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: P80375
#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 (bacteria) / Strain: HB8 / References: UniProt: P62654
#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 (bacteria) / Strain: HB8 / References: UniProt: P17293
#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 (bacteria) / Strain: HB8 / References: UniProt: P62655
#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 (bacteria) / Strain: HB8 / References: UniProt: P24320
#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 (bacteria) / Strain: HB8 / References: UniProt: P80378
#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 (bacteria) / Strain: HB8 / References: UniProt: P62238
#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 (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: P62659
#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 (bacteria) / Strain: HB8
#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 (bacteria) / Strain: HB8
#52: Protein/peptide 30S ribosomal protein Thx


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62612

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Non-polymers , 4 types, 1600 molecules

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


Mass: 24.305 Da / Num. of mol.: 1339 / 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.: 247 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 58.36 % / 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2018 / Details: S/N 60-0112-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→255.015 Å / Num. obs: 615531 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.501 % / Biso Wilson estimate: 123.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.209 / Χ2: 0.881 / Net I/σ(I): 5.59 / Num. measured all: 2154810 / Scaling rejects: 345
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
3.7-3.83.1431.4370.8614206445887452040.2491.72798.5
3.8-3.93.4931.1651.1415581044787446030.3731.37299.6
3.9-4.013.6090.9561.4215641743488433450.461.12199.7
4.01-4.143.6090.791.7215232142362422100.5640.92699.6
4.14-4.273.5810.6422.0814578340927407150.6570.75499.5
4.27-4.423.5490.5072.5614007739728394670.7490.59699.3
4.42-4.593.5310.4173.0813425538356380250.8130.4999.1
4.59-4.783.4590.343.6212544736817362690.8630.40298.5
4.78-4.993.2170.2784.1511142035466346360.8910.33297.7
4.99-5.233.5260.2255.3211813233863335040.9360.26598.9
5.23-5.523.6680.1926.2811723032267319620.9550.22499.1
5.52-5.853.6380.17710982430563301850.9640.19998.8
5.85-6.253.6170.1527.6510208128761282200.970.17898.1
6.25-6.763.510.138.569234926766263080.9760.15398.3
6.76-7.43.2550.09910.347773624720238800.9840.11896.6
7.4-8.273.5580.08113.027784522447218770.990.09597.5
8.27-9.553.6640.06915.617074319822193060.9920.08197.4
9.55-11.73.5940.05319.435865616901163220.9950.06396.6
11.7-16.553.270.04621.544062513193124240.9940.05594.2
16.55-255.0153.6770.04326.625995751970690.9950.05194

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2refinement
Coot0.8.2model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4P

4y4p


Resolution: 3.7→255.015 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 30948 5.03 %
Rwork0.2361 584231 -
obs0.2382 615179 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.88 Å2 / Biso mean: 103.7824 Å2 / Biso min: 50.23 Å2
Refinement stepCycle: final / Resolution: 3.7→255.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90996 195565 1599 15 288175
Biso mean--74.23 66.46 -
Num. residues----20661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003313004
X-RAY DIFFRACTIONf_angle_d0.635466774
X-RAY DIFFRACTIONf_chiral_restr0.03459086
X-RAY DIFFRACTIONf_plane_restr0.00425181
X-RAY DIFFRACTIONf_dihedral_angle_d13.625166209
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 (%)
3.7-3.7420.37839630.3393191962015998
3.742-3.78610.366510190.3286192812030098
3.7861-3.83230.358310600.3266194672052799
3.8323-3.88080.34329900.30791958520575100
3.8808-3.93180.334610070.29541966520672100
3.9318-3.98570.350810300.29691957220602100
3.9857-4.04270.327110100.29261956820578100
4.0427-4.1030.322910520.28621956120613100
4.103-4.16710.320410640.28271954620610100
4.1671-4.23540.347710630.2859195652062899
4.2354-4.30850.334810310.2822195872061899
4.3085-4.38680.326910330.2731195222055599
4.3868-4.47120.307410110.2664195452055699
4.4712-4.56250.283210670.249195092057699
4.5625-4.66170.2910570.2466193852044299
4.6617-4.77020.29310290.2413194002042998
4.7702-4.88950.307810290.2468193252035498
4.8895-5.02170.298110110.2432193222033398
5.0217-5.16940.290610660.2332194042047099
5.1694-5.33630.269310040.2197196232062799
5.3363-5.52710.263210690.214195632063299
5.5271-5.74840.259210270.2098195692059699
5.7484-6.010.264810620.214194392050198
6.01-6.32690.273510070.2184194652047298
6.3269-6.72330.270510270.2145195292055698
6.7233-7.24250.245410160.2078193602037697
7.2425-7.97130.247710400.2062192342027497
7.9713-9.12490.259810850.2119194992058498
9.1249-11.49640.214210020.1893194992050197
11.4964-255.62250.228410170.2037194462046394

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