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- PDB-4v4p: Crystal structure of 70S ribosome with thrS operator and tRNAs. -

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Basic information

Entry
Database: PDB / ID: 4v4p
TitleCrystal structure of 70S ribosome with thrS operator and tRNAs.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S ribosomal RNA
  • 50S general stress protein CTC (L25)
  • 5S ribosomal RNA
  • tRNA Phe (unmodified bases)
  • thrS mRNA operator
KeywordsRIBOSOME / mRNA / translational operator
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like ...Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein L2 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein L2, conserved site / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / 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 S8 signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL30 / 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 uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 5.5 Å
AuthorsJenner, L. / Romby, P. / Rees, B. / Schulze-Briese, C. / Springer, M. / Ehresmann, C. / Ehresmann, B. / Moras, D. / Yusupova, G. / Yusupov, M.
CitationJournal: Science / Year: 2005
Title: Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.
Authors: Jenner, L. / Romby, P. / Rees, B. / Schulze-Briese, C. / Springer, M. / Ehresmann, C. / Ehresmann, B. / Moras, D. / Yusupova, G. / Yusupov, M.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1YL3, 1YL4
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.3Sep 20, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 400COMPOUND PDB ENTRIES 1YL3 AND 1YL4 REPRESENT ONE CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS 70S ...COMPOUND PDB ENTRIES 1YL3 AND 1YL4 REPRESENT ONE CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME. THIS FILE, 1YL3, CONTAINS THE 50S SUBUNIT. THE 30S RIBOSOMAL SUBUNIT WITH MRNA AND TRNAS IS IN FILE 1YL4.
Remark 999SEQUENCE Initial C alpha coordinates of most proteins were those of PDB entry 1giy, which is the ...SEQUENCE Initial C alpha coordinates of most proteins were those of PDB entry 1giy, which is the same ribosome subunit from the same organism (Th. thermophilus). This was completed with proteins from 1nkw (same ribosome subunit from Deinococcus radiodurans), and structures of isolated proteins whenever available. The sequence of this subunit represent that of pdb entry 1giy. Proteins L20, L21, L25, L27, and L31 to L36 in the initial model were those of entry 1nkw and have the Deinococcus radiodurans sequence. The dbref is provided only for the sequences that match the relevant proteins from T. thermophilus. Residues (D ALA 216 ) and (D PRO 222 ) are linked together, Residues (E THR 49 ) and (E PRO 61 ) are linked together, Residues (E GLU 66 ) and (E THR 67 ) are linked together, Residues (E GLU 87 ) and (E GLN 93 ) are linked together, Residues (E ASN 190 ) and (E ILE 192 ) are linked together, Residues (E GLY 274 ) and (E GLY 291 ) are linked together, Residues (E ARG 312 ) and (E ALA 314 ) are linked together, Residues (F ASP 7 ) and (F ASN 11 ) are linked together, Residues (F ARG 168 ) and (F LEU 193 ) are linked together, Residues (F GLY 230 ) and (F ARG 231 ) are linked together, Residues (G GLY 107 ) and (G LEU 128 ) are linked together, Residues (K GLY 86 ) and (K ARG 88 ) are linked together, Residues (M PRO 88 ) and (M LYS 90 ) are linked together, Residues (O GLU 83 ) and (O ASP 92 ) are linked together, Residues (O VAL 96 ) and (O ALA 100 ) are linked together, Residues (Q THR 49 ) and (Q PRO 52 ) are linked together, Residues (Q GLU 72 ) and (Q PRO 74 ) are linked together, Residues (Q GLY 76 ) and (Q SER 80 ) are linked together, Residues (Q PRO 111 ) and (Q LYS 114 ) are linked together, Residues (R LEU 42 ) and (R ARG 44 ) are linked together, Residues (T PHE 20 ) and (T ASN 22 ) are linked together, Residues (T ASP 73 ) and (T GLN 75 ) are linked together, Residues (U GLY 36 ) and (U VAL 40 ) are linked together, Residues (W ARG 31 ) and (W VAL 33 ) are linked together.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AB: 5S ribosomal RNA
AA: 23S ribosomal RNA
AC: 50S ribosomal protein L1
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AI: 50S ribosomal protein L7/L12
AJ: 50S ribosomal protein L7/L12
AK: 50S ribosomal protein L9
AL: 50S ribosomal protein L11
AM: 50S ribosomal protein L13
AN: 50S ribosomal protein L14
AO: 50S ribosomal protein L15
AP: 50S ribosomal protein L16
AQ: 50S ribosomal protein L18
AR: 50S ribosomal protein L19
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S general stress protein CTC (L25)
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
A0: 50S ribosomal protein L17
A1: 50S ribosomal protein L20
A2: 50S ribosomal protein L21
A3: 50S ribosomal protein L27
A4: 50S ribosomal protein L31
A5: 50S ribosomal protein L32
A6: 50S ribosomal protein L33
A7: 50S ribosomal protein L34
A8: 50S ribosomal protein L35
A9: 50S ribosomal protein L36
BA: 16S rRNA
BB: tRNA Phe (unmodified bases)
BC: tRNA Phe (unmodified bases)
B1: thrS mRNA operator
BE: 30S ribosomal protein S2
BF: 30S ribosomal protein S3
BG: 30S ribosomal protein S4
BH: 30S ribosomal protein S5
BI: 30S ribosomal protein S6
BJ: 30S ribosomal protein S7
BK: 30S ribosomal protein S8
BL: 30S ribosomal protein S9
BM: 30S ribosomal protein S10
BN: 30S ribosomal protein S11
BO: 30S ribosomal protein S12
BP: 30S ribosomal protein S13
BQ: 30S ribosomal protein S14
BR: 30S ribosomal protein S15
BS: 30S ribosomal protein S16
BT: 30S ribosomal protein S17
BU: 30S ribosomal protein S18
BV: 30S ribosomal protein S19
BW: 30S ribosomal protein S20
BX: 30S ribosomal protein Thx


Theoretical massNumber of molelcules
Total (without water)2,308,73658
Polymers2,308,73658
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)508.640, 508.640, 806.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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RNA chain , 5 types, 6 molecules ABAABABBBCB1

#1: RNA chain 5S ribosomal RNA


Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48271
#2: RNA chain 23S ribosomal RNA


Mass: 947975.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48268
#34: RNA chain 16S rRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: GenBank: 155076
#35: RNA chain tRNA Phe (unmodified bases)


Mass: 24518.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER
#36: RNA chain thrS mRNA operator


Mass: 24992.760 Da / Num. of mol.: 1
Fragment: nucleotides -59 to +19 of thrS mRNA (here renumbered 1 to 77)
Source method: obtained synthetically
Details: T7 transcript of the E.coli thrmRNA 78 nuc fragment
Keywords: MONOMER

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50S ribosomal protein ... , 30 types, 31 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAWAXA0A1A2A3A4A5A6A7A8A9

#3: Protein 50S ribosomal protein L1


Mass: 24736.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27150
#4: Protein 50S ribosomal protein L2


Mass: 19283.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#5: Protein 50S ribosomal protein L3


Mass: 37412.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#6: Protein 50S ribosomal protein L4


Mass: 26443.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#7: Protein 50S ribosomal protein L5


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#8: Protein 50S ribosomal protein L6


Mass: 19202.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#9: Protein 50S ribosomal protein L7/L12


Mass: 13475.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#10: Protein 50S ribosomal protein L9


Mass: 16341.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#11: Protein 50S ribosomal protein L11


Mass: 15111.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#12: Protein 50S ribosomal protein L13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#13: Protein 50S ribosomal protein L14


Mass: 13369.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#14: Protein 50S ribosomal protein L15


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#15: Protein 50S ribosomal protein L16


Mass: 15313.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#16: Protein 50S ribosomal protein L18


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#17: Protein 50S ribosomal protein L19


Mass: 7233.720 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P48286, UniProt: Q5SHP3*PLUS
#19: Protein 50S ribosomal protein L23


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#20: Protein 50S ribosomal protein L24


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#22: Protein 50S ribosomal protein L29


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#23: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P74909, UniProt: Q5SHQ6*PLUS
#24: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#25: Protein 50S ribosomal protein L20


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#26: Protein 50S ribosomal protein L21


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#27: Protein 50S ribosomal protein L27


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#28: Protein 50S ribosomal protein L31


Mass: 8597.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#29: Protein 50S ribosomal protein L32


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#30: Protein 50S ribosomal protein L33


Mass: 9294.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#31: Protein/peptide 50S ribosomal protein L34


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#32: Protein 50S ribosomal protein L35


Mass: 7261.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4265.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

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Protein , 1 types, 1 molecules AV

#21: Protein 50S general stress protein CTC (L25)


Mass: 27004.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

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30S ribosomal protein ... , 20 types, 20 molecules BEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBX

#37: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: P80371
#38: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHP4, UniProt: P80372*PLUS
#39: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHR5, UniProt: P80373*PLUS
#40: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHQ5
#41: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SLP8
#42: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHN4, UniProt: P17291*PLUS
#43: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#44: Protein 30S ribosomal protein S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SIB0, UniProt: P80374*PLUS
#45: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHN7
#46: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: P80376
#47: Protein 30S ribosomal protein S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Keywords: MONOMER / References: UniProt: Q5SHN3
#48: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: P80377
#49: Protein 30S ribosomal protein S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#50: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SJ76
#51: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SJH3
#52: Protein 30S ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Keywords: MONOMER / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#53: Protein 30S ribosomal protein S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SLQ0
#54: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SHP2
#55: Protein 30S ribosomal protein S20


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SIH2, UniProt: P80380*PLUS
#56: Protein/peptide 30S ribosomal protein Thx


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / Keywords: MONOMER / References: UniProt: Q5SIH3

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 87.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2H2O11
3MPD12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 2004 / Details: Dynamically Bendable Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 5.5→300 Å / Num. obs: 165570 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 1.047 / Net I/σ(I): 13.9
Reflection shellResolution: 5.5→5.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.83 / Num. unique all: 7889 / Χ2: 1.573 / % possible all: 94.2

-
Processing

Software
NameClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30

1giy
PDB Unreleased entry

1nkw

1ad2

1gd8

1bxe

1bxy


Resolution: 5.5→300 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.356 7724 4.6 %random
Rwork0.307 ---
all0.314 165002 --
obs0.309 160401 94.6 %-
Displacement parametersBiso mean: 204 Å2
Refinement stepCycle: LAST / Resolution: 5.5→300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27609 64488 0 0 92097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_mcbond_it1
X-RAY DIFFRACTIONc_mcangle_it1.7
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
5.5-5.840.466512420.4383X-RAY DIFFRACTION91.9
5.84-6.30.419912220.3572X-RAY DIFFRACTION91.7
6.3-6.930.395512740.3153X-RAY DIFFRACTION95.5
6.93-7.930.384812950.2849X-RAY DIFFRACTION95.9
7.93-9.990.376413030.2973X-RAY DIFFRACTION96.1
9.99-3000.316513880.2916X-RAY DIFFRACTION96.3

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