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- PDB-4v42: Crystal structure of the ribosome at 5.5 A resolution. -

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Entry
Database: PDB / ID: 4v42
TitleCrystal structure of the ribosome at 5.5 A resolution.
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 21
  • (TRNA(PHE)) x 2
  • 30S 16S RIBOSOMAL RNA
  • 50S 23S RIBOSOMAL RNA
  • 50S 5S RIBOSOMAL RNA
  • A- AND P-SITE MESSENGER RNA CODONS
KeywordsRIBOSOME / ribosome assembly / protein synthesis / life
Function / homology
Function and homology information


response to radiation / large ribosomal subunit / regulation of translation / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly ...response to radiation / large ribosomal subunit / regulation of translation / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain ...Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L1, bacterial-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein S14, type Z / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L25, short-form / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / 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 L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / 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 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 L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily
Similarity search - Domain/homology
: / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...: / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L10e / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL9 / 50S ribosomal protein L25 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / 30S ribosomal protein Thx / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL25 / 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 uS19 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 5.5 Å
AuthorsYusupov, M.M. / Yusupova, G.Z. / Baucom, A. / Lieberman, K. / Earnest, T.N. / Cate, J.H.D. / Noller, H.F.
CitationJournal: Science / Year: 2001
Title: Crystal structure of the ribosome at 5.5 A resolution
Authors: Yusupov, M.M. / Yusupova, G.Z. / Baucom, A. / Lieberman, K. / Earnest, T.N. / Cate, J.H.D. / Noller, H.F.
History
DepositionMar 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1GIX, 1GIY
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 30S 16S RIBOSOMAL RNA
AB: TRNA(PHE)
AC: TRNA(PHE)
AD: TRNA(PHE)
A1: A- AND P-SITE MESSENGER RNA CODONS
AE: 30S RIBOSOMAL PROTEIN S2
AF: 30S RIBOSOMAL PROTEIN S3
AG: 30S RIBOSOMAL PROTEIN S4
AH: 30S RIBOSOMAL PROTEIN S5
AI: 30S RIBOSOMAL PROTEIN S6
AJ: 30S RIBOSOMAL PROTEIN S7
AK: 30S RIBOSOMAL PROTEIN S8
AL: 30S RIBOSOMAL PROTEIN S9
AM: 30S RIBOSOMAL PROTEIN S10
AN: 30S RIBOSOMAL PROTEIN S11
AO: 30S RIBOSOMAL PROTEIN S12
AP: 30S RIBOSOMAL PROTEIN S13
AQ: 30S RIBOSOMAL PROTEIN S14
AR: 30S RIBOSOMAL PROTEIN S15
AS: 30S RIBOSOMAL PROTEIN S16
AT: 30S RIBOSOMAL PROTEIN S17
AU: 30S RIBOSOMAL PROTEIN S18
AV: 30S RIBOSOMAL PROTEIN S19
AW: 30S RIBOSOMAL PROTEIN S20
AX: 30S RIBOSOMAL PROTEIN THX
BA: 50S 23S RIBOSOMAL RNA
BB: 50S 5S RIBOSOMAL RNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BI: 50S RIBOSOMAL PROTEIN L7/L12
BJ: 50S RIBOSOMAL PROTEIN L7/L12
BK: 50S RIBOSOMAL PROTEIN L9
BL: 50S RIBOSOMAL PROTEIN L11
BM: 50S RIBOSOMAL PROTEIN L13
BN: 50S RIBOSOMAL PROTEIN L14
BO: 50S RIBOSOMAL PROTEIN L15
BP: 50S RIBOSOMAL PROTEIN L16
BQ: 50S RIBOSOMAL PROTEIN L18
BR: 50S RIBOSOMAL PROTEIN L19
BS: 50S RIBOSOMAL PROTEIN L22
BT: 50S RIBOSOMAL PROTEIN L23
BU: 50S RIBOSOMAL PROTEIN L24
BV: 50S RIBOSOMAL PROTEIN L25
BW: 50S RIBOSOMAL PROTEIN L29
BX: 50S RIBOSOMAL PROTEIN L30


Theoretical massNumber of molelcules
Total (without water)2,203,91549
Polymers2,203,91549
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)507.20, 507.20, 803.66
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number97
Cell settingtetragonal
Space group name H-MI422

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Components

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RNA chain , 6 types, 7 molecules AAABACADA1BABB

#1: RNA chain 30S 16S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076
#2: RNA chain TRNA(PHE)


Mass: 24890.121 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: sequence naturally occurs in Saccharomyces cerevisiae
References: GenBank: 176479
#3: RNA chain TRNA(PHE)


Mass: 23728.123 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence naturally occurs in Saccharomyces cerevisiae
#4: RNA chain A- AND P-SITE MESSENGER RNA CODONS


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 6 NT LONG MRNA FRAGMENT
#25: RNA chain 50S 23S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 48268
#26: RNA chain 50S 5S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 176261

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules AEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAX

#5: Protein 30S RIBOSOMAL PROTEIN S2 / Coordinate model: Cα atoms only


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371
#6: Protein 30S RIBOSOMAL PROTEIN S3 / Coordinate model: Cα atoms only


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62663, UniProt: P80372*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S4 / Coordinate model: Cα atoms only


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373
#8: Protein 30S RIBOSOMAL PROTEIN S5 / Coordinate model: Cα atoms only


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ5
#9: Protein 30S RIBOSOMAL PROTEIN S6 / Coordinate model: Cα atoms only


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP8
#10: Protein 30S RIBOSOMAL PROTEIN S7 / Coordinate model: Cα atoms only


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#11: Protein 30S RIBOSOMAL PROTEIN S8 / Coordinate model: Cα atoms only


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S9 / Coordinate model: Cα atoms only


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80374
#13: Protein 30S RIBOSOMAL PROTEIN S10 / Coordinate model: Cα atoms only


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN7
#14: Protein 30S RIBOSOMAL PROTEIN S11 / Coordinate model: Cα atoms only


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376
#15: Protein 30S RIBOSOMAL PROTEIN S12 / Coordinate model: Cα atoms only


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3
#16: Protein 30S RIBOSOMAL PROTEIN S13 / Coordinate model: Cα atoms only


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377
#17: Protein 30S RIBOSOMAL PROTEIN S14 / Coordinate model: Cα atoms only


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S15 / Coordinate model: Cα atoms only


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJ76
#19: Protein 30S RIBOSOMAL PROTEIN S16 / Coordinate model: Cα atoms only


Mass: 10808.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 12056104, UniProt: Q5SJH3*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S17 / Coordinate model: Cα atoms only


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P0DOY7*PLUS
#21: Protein 30S RIBOSOMAL PROTEIN S18 / Coordinate model: Cα atoms only


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS
#22: Protein 30S RIBOSOMAL PROTEIN S19 / Coordinate model: Cα atoms only


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#23: Protein 30S RIBOSOMAL PROTEIN S20 / Coordinate model: Cα atoms only


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS
#24: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Coordinate model: Cα atoms only


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P32193, UniProt: Q5SIH3*PLUS

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50S RIBOSOMAL PROTEIN ... , 21 types, 22 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBX

#27: Protein 50S RIBOSOMAL PROTEIN L1 / Coordinate model: Cα atoms only


Mass: 24736.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27150, UniProt: Q5SLP7*PLUS
#28: Protein 50S RIBOSOMAL PROTEIN L2 / Coordinate model: Cα atoms only


Mass: 19283.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P04257, UniProt: P20276
#29: Protein 50S RIBOSOMAL PROTEIN L3 / Coordinate model: Cα atoms only


Mass: 37412.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P20279
#30: Protein 50S RIBOSOMAL PROTEIN L4 / Coordinate model: Cα atoms only


Mass: 26443.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P12735
#31: Protein 50S RIBOSOMAL PROTEIN L5 / Coordinate model: Cα atoms only


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P14124
#32: Protein 50S RIBOSOMAL PROTEIN L6 / Coordinate model: Cα atoms only


Mass: 19202.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P02391
#33: Protein 50S RIBOSOMAL PROTEIN L7/L12 / Coordinate model: Cα atoms only


Mass: 13475.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P29396
#34: Protein 50S RIBOSOMAL PROTEIN L9 / Coordinate model: Cα atoms only


Mass: 16341.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P02417
#35: Protein 50S RIBOSOMAL PROTEIN L11 / Coordinate model: Cα atoms only


Mass: 15111.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P29395
#36: Protein 50S RIBOSOMAL PROTEIN L13 / Coordinate model: Cα atoms only


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P29198
#37: Protein 50S RIBOSOMAL PROTEIN L14 / Coordinate model: Cα atoms only


Mass: 13369.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P04450
#38: Protein 50S RIBOSOMAL PROTEIN L15 / Coordinate model: Cα atoms only


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P12737
#39: Protein 50S RIBOSOMAL PROTEIN L16 / Coordinate model: Cα atoms only


Mass: 15313.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: A0A0X1KGB2*PLUS
#40: Protein 50S RIBOSOMAL PROTEIN L18 / Coordinate model: Cα atoms only


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P14123
#41: Protein 50S RIBOSOMAL PROTEIN L19 / Coordinate model: Cα atoms only


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P14116
#42: Protein 50S RIBOSOMAL PROTEIN L22 / Coordinate model: Cα atoms only


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P48286, UniProt: Q5SHP3*PLUS
#43: Protein 50S RIBOSOMAL PROTEIN L23 / Coordinate model: Cα atoms only


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P12732
#44: Protein 50S RIBOSOMAL PROTEIN L24 / Coordinate model: Cα atoms only


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P10972
#45: Protein 50S RIBOSOMAL PROTEIN L25 / Coordinate model: Cα atoms only


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P02426, UniProt: P68919*PLUS
#46: Protein 50S RIBOSOMAL PROTEIN L29 / Coordinate model: Cα atoms only


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P10971
#47: Protein 50S RIBOSOMAL PROTEIN L30 / Coordinate model: Cα atoms only


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P74909, UniProt: Q5SHQ6*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.86 Å3/Da / Density % sol: 79.02 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 5→250 Å / Num. all: 209044 / Num. obs: 209044 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.094
Reflection shellResolution: 5.5→5.7 Å / % possible obs: 95 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.308 / % possible all: 95

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
Omodel building
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 5.5→250 Å / σ(I): 0
Details: THE MODEL WAS BUILT BY MANUAL FITTING OF INDIVIDUAL MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O.
Num. reflection% reflection
all209044 -
obs209044 95.3 %
Refinement stepCycle: LAST / Resolution: 5.5→250 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 6513 0 0 8909

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