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- PDB-4v4s: Crystal structure of the whole ribosomal complex. -

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Basic information

Entry
Database: PDB / ID: 4v4s
TitleCrystal structure of the whole ribosomal complex.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*AP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'
  • 5S ribosomal RNA
  • E-site tRNA (Phe)
  • P-site tRNA (Phe)
  • Peptide chain release factor 2
KeywordsRIBOSOME / translation / release factor
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding ...translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / 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 / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / : ...Peptide chain release factor 2 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / : / Peptide chain release factor class I / RF-1 domain / 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 L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein S14, type Z / metallochaperone-like domain / TRASH domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L13, eukaryotic/archaeal / 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 L31 type A / 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 L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 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 / Ribosomal protein L9, N-terminal domain superfamily / 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 L35, non-mitochondrial / : / Ribosomal protein L6, bacterial-type / 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 S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L27, conserved site
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS14 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL9 / 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 uL3 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS9 / 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 uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / 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 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Peptide chain release factor RF2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.76 Å
AuthorsPetry, S. / Brodersen, D.E. / Murphy IV, F.V. / Dunham, C.M. / Selmer, M. / Tarry, M.J. / Kelley, A.C. / Ramakrishnan, V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.
Authors: Petry, S. / Brodersen, D.E. / Murphy IV, F.V. / Dunham, C.M. / Selmer, M. / Tarry, M.J. / Kelley, A.C. / Ramakrishnan, V.
History
DepositionOct 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2B9M, 2B9N
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_ref_seq_dif.details
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / ndb_struct_conf_na ...database_PDB_caveat / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Remark 400COMPOUND THIS FILE, 2B9M, CONTAINS THE 30S SUBUNIT , TRNAS, MRNA AND RELEASE FACTOR RF2 FROM A ...COMPOUND THIS FILE, 2B9M, CONTAINS THE 30S SUBUNIT , TRNAS, MRNA AND RELEASE FACTOR RF2 FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX. THE ENTIRE CRYSTAL STRUCTURE CONTAIN ONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTOR RF2 AND ARE DEPOSITED UNDER 2B9M (30S SUBUNIT AND LIGANDS) AND 2B9N (50S SUBUNIT).
Remark 999SEQUENCE THE FIRST 17 INSERTIONS IN CHAIN Y ARE DUE TO AN INTERNAL FRAMESHIFT SITE WITHIN THE RF2 ...SEQUENCE THE FIRST 17 INSERTIONS IN CHAIN Y ARE DUE TO AN INTERNAL FRAMESHIFT SITE WITHIN THE RF2 (CHAIN Y) CODING SEQUENCE. THE +1 FRAMESHIFT TAKES PLACE AT POSITION 18.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AV: P-site tRNA (Phe)
AW: E-site tRNA (Phe)
AX: 5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*AP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AY: Peptide chain release factor 2
BB: 5S ribosomal RNA
BA: 23S ribosomal RNA
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 L9
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein 24
BZ: 50S ribosomal protein CTC
BR: 50S ribosomal protein L17
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B0: 50S ribosomal protein L27
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
B9: 50S ribosomal protein L36
BK: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)2,279,13556
Polymers2,279,13556
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)520.213, 520.213, 365.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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RNA chain , 6 types, 6 molecules AAAVAWAXBBBA

#1: RNA chain 16S ribosomal RNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076
#2: RNA chain P-site tRNA (Phe)


Mass: 24518.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBs tRNAPhe / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174
#3: RNA chain E-site tRNA (Phe)


Mass: 24743.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBs tRNAPhe / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174
#4: RNA chain 5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*AP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'


Mass: 5703.420 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHEMICALLY SYNTHESIZED AND GEL-PURIFIED SOURCE 24 (DHARMACON)
#26: 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) / References: GenBank: 48271
#27: RNA chain 23S ribosomal RNA


Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48268

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

#5: 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 / References: UniProt: P80371
#6: Protein 30S ribosomal protein S3 / TS9


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#7: 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 / References: UniProt: P80373
#8: 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 / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#9: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#10: 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 / References: UniProt: P17291
#11: 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 / References: UniProt: P24319, UniProt: P0DOY9*PLUS
#12: 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 / References: UniProt: P62669, UniProt: P80374*PLUS
#13: 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 / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#14: 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 / References: UniProt: P80376
#15: Protein 30S ribosomal protein S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55981666, UniProt: Q5SHN3*PLUS
#16: 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 / References: UniProt: P80377
#17: 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 / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#18: 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 / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#19: 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 / References: UniProt: Q5SJH3
#20: Protein 30S ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24321, UniProt: P0DOY7*PLUS
#21: 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 / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS
#22: 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 / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#23: 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 / References: UniProt: P62661, UniProt: P80380*PLUS
#24: 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 / References: UniProt: P62612, UniProt: Q5SIH3*PLUS

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Protein , 1 types, 1 molecules AY

#25: Protein Peptide chain release factor 2 / RF-2 / Coordinate model: Cα atoms only


Mass: 41475.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prfA / Plasmid: pET42bTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM01

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50S ribosomal protein ... , 29 types, 29 molecules BDBEBFBGBHBIBNBOBPBQBSBTBWBXBYBZBRBUBVB2B3B0B4B5B6B7B8B9BK

#28: Protein 50S ribosomal protein L2


Mass: 18652.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5L3Z4*PLUS
#29: 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) / References: UniProt: P20279*PLUS
#30: 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) / References: UniProt: P12735*PLUS
#31: 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) / References: UniProt: P14124*PLUS
#32: 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) / References: UniProt: Q5L408*PLUS
#33: 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) / References: UniProt: P02417*PLUS
#34: 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) / References: UniProt: P29198*PLUS
#35: 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) / References: UniProt: Q5L413*PLUS
#36: 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) / References: UniProt: P12737*PLUS
#37: 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)
#38: 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) / References: UniProt: P14123*PLUS
#39: 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) / References: UniProt: P14116*PLUS
#40: 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) / References: UniProt: P48286, UniProt: Q5SHP3*PLUS
#41: 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) / References: UniProt: P12732*PLUS
#42: Protein 50S ribosomal protein 24


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P10972*PLUS
#43: Protein 50S ribosomal protein CTC


Mass: 27004.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q9RX88*PLUS
#44: 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) / References: UniProt: Q9Z9H5
#45: 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) / References: UniProt: Q9RSW7*PLUS
#46: 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) / References: UniProt: Q9RY64*PLUS
#47: 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) / References: UniProt: P10971*PLUS
#48: 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) / References: UniProt: P74909, UniProt: Q5SHQ6*PLUS
#49: 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) / References: UniProt: Q9RY65*PLUS
#50: 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) / References: UniProt: Q9RW44*PLUS
#51: 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) / References: UniProt: P49228*PLUS
#52: 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) / References: UniProt: Q9RSS4*PLUS
#53: 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) / References: UniProt: Q9RSH2*PLUS
#54: 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) / References: UniProt: Q9RSW6*PLUS
#55: 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) / References: UniProt: Q9RSK0*PLUS
#56: 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) / References: UniProt: P29395*PLUS

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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: 5

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.7
Details: PEG20k, MES buffer, magnesium acetate, potassium chloride, ammonium chloride, pH 6.7, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG20K11
2MES11
3magnesium acetate11
4potassium chloride11
5ammonium chloride11
6H2O11
7PEG20K12
8magnesium acetate12
9potassium chloride12
10ammonium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976269 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2005
RadiationMonochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976269 Å / Relative weight: 1
ReflectionResolution: 6.76→100 Å / Num. obs: 123564 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 5.7 % / Rsym value: 0.193 / Net I/σ(I): 8.2
Reflection shellResolution: 6.76→7.11 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.34 / Num. unique all: 12215 / Rsym value: 0.75 / % possible all: 99.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J5E, 1NKW

1j5e

1nkw


Resolution: 6.76→43.35 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 31449976.91 / Stereochemistry target values: Engh & Huber
Details: THIS IS A LOW RESOLUTION STRUCTURE OBTAINED BY USING A MOLECULAR REPLACEMENT MODEL. THE STRUCTURE IS DEPOSITED AS AN ALL-ATOM MODEL ONLY SO THAT OUR REFINEMENT PROCEDURE AND MAPS CAN BE ...Details: THIS IS A LOW RESOLUTION STRUCTURE OBTAINED BY USING A MOLECULAR REPLACEMENT MODEL. THE STRUCTURE IS DEPOSITED AS AN ALL-ATOM MODEL ONLY SO THAT OUR REFINEMENT PROCEDURE AND MAPS CAN BE REPLICATED. THE CONFORMATION OF INDIVIDUAL ATOMS OR SIDE CHAINS, THE REGISTRY OF THE RESIDUES ALONG THE CHAIN, OR EVEN THE DETAILED PATH OF MAIN CHAINS CANNOT BE ASCERTAINED AT THIS RESOLUTION. Chain AX contains only P atoms and chain AY contains only CA atoms. There are lots of O3*-P distances that are not within bond distance in both chain AA and chain AW.
RfactorNum. reflection% reflectionSelection details
Rfree0.356 4219 -random
Rwork0.341 ---
all0.344 ---
obs0.344 84085 96.2 %-
Displacement parametersBiso mean: 279 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.5 Å1.39 Å
Luzzati d res low-15 Å
Luzzati sigma a1.29 Å0.92 Å
Refinement stepCycle: LAST / Resolution: 6.76→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19596 35947 0 0 55543
LS refinement shellResolution: 6.76→6.81 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.399 629 -
Rwork0.367 --
obs--87.9 %

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