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- PDB-5f8k: Crystal structure of the Bac7(1-16) antimicrobial peptide bound t... -

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Basic information

Entry
Database: PDB / ID: 5f8k
TitleCrystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus thermophilus 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Cathelicidin-3
  • mRNA
  • tRNAiMet
KeywordsRIBOSOME / bacterial ribosome / proline-rich antimicrobial peptide / antibiotics / protein biosynthesis
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / defense response to bacterium / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / extracellular region / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form ...Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily / 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 L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / 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 / Cathelicidin-3 / 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 / 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)
synthetic construct (others)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
Authors: Seefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / 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.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_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.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.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.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
Revision 1.4Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order
Revision 1.5Mar 12, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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

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: tRNAiMet
1y: Cathelicidin-3
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: tRNAiMet
2y: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,404,6602829
Polymers4,337,397110
Non-polymers67,2632719
Water87,3014846
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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: tRNAiMet
1y: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,202,6101426
Polymers2,168,69955
Non-polymers33,9111371
Water70339
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: tRNAiMet
2y: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,202,0511403
Polymers2,168,69955
Non-polymers33,3521348
Water68538
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.960, 450.130, 622.820
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 , 5 types, 10 molecules 1A2A1B2B1a2a1v2v1x2x

#1: RNA chain 23S ribosomal RNA


Mass: 948007.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S ribosomal RNA


Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#32: RNA chain 16S ribosomal RNA


Mass: 493558.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#53: RNA chain mRNA


Mass: 935.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#54: RNA chain tRNAiMet


Mass: 24541.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Plasmid: pBS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

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

#3: Protein 50S ribosomal protein L2


Mass: 30401.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60405
#4: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN8
#5: Protein 50S ribosomal protein L4 / L1e


Mass: 22512.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN9
#6: Protein 50S ribosomal protein L5


Mass: 20930.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ0
#7: Protein 50S ribosomal protein L6


Mass: 18980.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#8: Protein 50S ribosomal protein L9


Mass: 16293.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / 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 / Details: cell / 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 / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP8
#11: Protein 50S ribosomal protein L15


Mass: 16248.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / 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 / Details: cell / 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 / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9Z9H5
#14: Protein 50S ribosomal protein L18 / TL24


Mass: 12437.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ4
#15: Protein 50S ribosomal protein L19


Mass: 15503.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60490
#16: Protein 50S ribosomal protein L20


Mass: 13591.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / 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 / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60492
#18: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP3
#19: Protein 50S ribosomal protein L23


Mass: 10646.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP0
#20: Protein 50S ribosomal protein L24


Mass: 11726.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP9
#21: Protein 50S ribosomal protein L25 / TL5


Mass: 22851.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHZ1
#22: Protein 50S ribosomal protein L27


Mass: 8689.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60493
#23: Protein 50S ribosomal protein L28


Mass: 10872.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60494
#24: Protein 50S ribosomal protein L29


Mass: 8485.077 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP6
#25: Protein 50S ribosomal protein L30


Mass: 6667.931 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ6
#26: Protein 50S ribosomal protein L31


Mass: 8086.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJE1
#27: Protein 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80339
#28: Protein 50S ribosomal protein L33


Mass: 6501.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P35871
#29: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80340
#30: Protein 50S ribosomal protein L35


Mass: 7374.981 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / 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 / Details: cell / 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: 26646.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371
#34: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372
#35: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373
#36: Protein 30S ribosomal protein S5


Mass: 16144.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#37: Protein 30S ribosomal protein S6 / TS9


Mass: 11917.675 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8
#38: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291
#39: Protein 30S ribosomal protein S8


Mass: 15737.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#40: Protein 30S ribosomal protein S9


Mass: 14279.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374
#41: Protein 30S ribosomal protein S10


Mass: 11169.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7
#42: Protein 30S ribosomal protein S11


Mass: 12032.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376
#43: Protein 30S ribosomal protein S12


Mass: 13650.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3
#44: Protein 30S ribosomal protein S13


Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#45: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#46: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76
#47: Protein 30S ribosomal protein S16


Mass: 9795.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3
#48: Protein 30S ribosomal protein S17


Mass: 11722.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#49: Protein 30S ribosomal protein S18


Mass: 7897.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0
#50: Protein 30S ribosomal protein S19


Mass: 9455.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2
#51: Protein 30S ribosomal protein S20


Mass: 10876.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#52: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 2831.295 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/peptide , 1 types, 2 molecules 1y2y

#55: Protein/peptide Cathelicidin-3 / Bactenecin-7 / Bac7 / PR-59


Mass: 2084.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P19661

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Non-polymers , 5 types, 7565 molecules

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


Mass: 24.305 Da / Num. of mol.: 2703 / 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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#60: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4846 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Tris-HCl, PEG 20000, MPD, Arginine

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 1422951 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.03 Å2 / Rmerge F obs: 0.957 / Rmerge(I) obs: 0.512 / Rrim(I) all: 0.545 / Χ2: 0.853 / Net I/σ(I): 5.71 / Num. measured all: 11868574
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.970.1612.3390.9618121152293692238202.49697.6
2.97-3.170.4081.3491.8518213742158802158201.436100
3.17-3.430.6230.8633.0816965892009702009110.918100
3.43-3.750.7710.6294.3615633371853191852740.67100
3.75-4.190.8810.4436.314145421678831678360.472100
4.19-4.830.940.3228.4812470821484831484700.343100
4.83-5.910.9680.24810.410527821260441260430.264100
5.91-8.290.9830.19512.0280159398339982660.20899.9
8.290.9980.07622.645916056910565110.08299.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4O

4y4o


Resolution: 2.8→48.625 Å / FOM work R set: 0.7657 / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 70175 4.94 %
Rwork0.2488 1351698 -
obs0.2509 1421873 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.12 Å2 / Biso mean: 44.05 Å2 / Biso min: 3.54 Å2
Refinement stepCycle: final / Resolution: 2.8→48.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91793 196736 7673 36 296238
Biso mean--35.05 23.74 -
Num. residues----20805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019327348
X-RAY DIFFRACTIONf_angle_d1.073476221
X-RAY DIFFRACTIONf_chiral_restr0.05459475
X-RAY DIFFRACTIONf_plane_restr0.00525387
X-RAY DIFFRACTIONf_dihedral_angle_d14.746145683
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 (%)
2.8001-2.83190.412320980.3899398404193889
2.8319-2.86520.394223670.36934496347330100
2.8652-2.90010.388223660.36344495147317100
2.9001-2.93680.388623650.35294493947304100
2.9368-2.97550.385623710.35064505447425100
2.9755-3.01620.386923680.35344499947367100
3.0162-3.05930.370923690.32854499447363100
3.0593-3.1050.361519330.31534547547408100
3.105-3.15350.349523090.30284506647375100
3.1535-3.20520.335323480.29794508747435100
3.2052-3.26040.341423620.29494504747409100
3.2604-3.31970.334823540.28124508947443100
3.3197-3.38350.320823870.27424513247519100
3.3835-3.45260.317923470.2694503947386100
3.4526-3.52760.30923570.26374513347490100
3.5276-3.60970.301223460.25694514247488100
3.6097-3.69990.295623470.24994515447501100
3.6999-3.79990.294423660.24724516647532100
3.7999-3.91170.283123560.23774522347579100
3.9117-4.03790.287623560.23714528347639100
4.0379-4.18210.274423780.22674511047488100
4.1821-4.34950.266823310.22344527647607100
4.3495-4.54730.266723920.21964534747739100
4.5473-4.78680.246723630.20754534147704100
4.7868-5.08650.247823500.20354540247752100
5.0865-5.47870.241223810.19454543447815100
5.4787-6.02910.239323780.18994558247960100
6.0291-6.89940.235223920.18554570148093100
6.8994-8.68450.220923670.17974586648233100
8.6845-48.63260.238823710.218458634823498

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