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- PDB-4v8o: Crystal structure of the hybrid state of ribosome in complex with... -

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Basic information

Entry
Database: PDB / ID: 4v8o
TitleCrystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 16S RRNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • MRNA 5'-R(*AP*AP*AP*AP*AP*AP*UP*GP*UP)-3'
  • PE HYBRID STATE TRNA FMET
  • PEPTIDE CHAIN RELEASE FACTOR 3
KeywordsRIBOSOME / HYBRID STATE / P/E TRNA / GUANOSINE TRIPHOSPHATASE / RELEASE FACTOR 3
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon specific / guanosine tetraphosphate binding / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit ...regulation of translational termination / translation release factor activity, codon specific / guanosine tetraphosphate binding / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / : / Elongation factor G domain 2 / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / : / Elongation factor G domain 2 / Ribosomal protein L1, bacterial-type / 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 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / 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 / Elongation factor Tu domain 2 / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein L20 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / 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 L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / : / L28p-like
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Peptide chain release factor 3 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Peptide chain release factor 3 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / 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 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsJin, H. / Kelley, A.C. / Ramakrishnan, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal Structure of the Hybrid State of Ribosome in Complex with the Guanosine Triphosphatase Release Factor 3.
Authors: Jin, H. / Kelley, A.C. / Ramakrishnan, V.
History
DepositionJul 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3ZVO, 3ZVP
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / struct_conn / struct_conn_type
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 / pdbx_initial_refinement_model / struct_conn
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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S RRNA
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 TYPE Z
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
AV: PE HYBRID STATE TRNA FMET
AX: MRNA 5'-R(*AP*AP*AP*AP*AP*AP*UP*GP*UP)-3'
AY: PEPTIDE CHAIN RELEASE FACTOR 3
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
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
BA: 23S RIBOSOMAL RNA
BB: 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
BJ: 50S RIBOSOMAL PROTEIN L10
BK: 50S RIBOSOMAL PROTEIN L11
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,292,76158
Polymers2,292,24057
Non-polymers5211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.700, 229.300, 307.000
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 5 types, 5 molecules AAAVAXBABB

#1: RNA chain 16S RRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AVY.
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: GenBank: 55979969
#22: RNA chain PE HYBRID STATE TRNA FMET


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12
#23: RNA chain MRNA 5'-R(*AP*AP*AP*AP*AP*AP*UP*GP*UP)-3'


Mass: 2887.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#35: RNA chain 23S RIBOSOMAL RNA


Mass: 947975.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: GenBank: 55979969
#36: RNA chain 5S RIBOSOMAL RNA


Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: GenBank: 55979969

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

#2: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80371
#3: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80372
#4: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80373
#5: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ5
#6: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SLP8
#7: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P17291
#8: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80374
#10: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHN7
#11: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80376
#12: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHN3
#13: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80377
#14: Protein 30S RIBOSOMAL PROTEIN S14 TYPE Z


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SJ76
#16: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SLQ0
#19: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80380
#21: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SIH3

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50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules B0B1B2B3B4B5B6B7B8B9BCBDBEBFBGBHBJBKBNBOBPBQBRBSBTBUBVBWBXBYBZ

#25: Protein 50S RIBOSOMAL PROTEIN L27


Mass: 9529.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60493
#26: Protein 50S RIBOSOMAL PROTEIN L28


Mass: 11004.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60494
#27: Protein 50S RIBOSOMAL PROTEIN L29


Mass: 8670.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP6
#28: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ6
#29: Protein 50S RIBOSOMAL PROTEIN L31


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SJE1
#30: Protein 50S RIBOSOMAL PROTEIN L32


Mass: 6722.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80339
#31: Protein 50S RIBOSOMAL PROTEIN L33


Mass: 6632.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P35871
#32: Protein/peptide 50S RIBOSOMAL PROTEIN L34


Mass: 6132.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P80340
#33: Protein 50S RIBOSOMAL PROTEIN L35


Mass: 7506.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SKU1
#34: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / RIBOSOMAL PROTEIN B


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHR2
#37: Protein 50S RIBOSOMAL PROTEIN L1


Mass: 24885.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SLP7
#38: Protein 50S RIBOSOMAL PROTEIN L2


Mass: 30532.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60405
#39: Protein 50S RIBOSOMAL PROTEIN L3


Mass: 22450.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHN8
#40: Protein 50S RIBOSOMAL PROTEIN L4


Mass: 23271.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHN9
#41: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ0
#42: Protein 50S RIBOSOMAL PROTEIN L6


Mass: 19568.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#43: Protein 50S RIBOSOMAL PROTEIN L10


Mass: 14769.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8
#44: Protein 50S RIBOSOMAL PROTEIN L11


Mass: 12528.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BUILT AS POLY-ALA / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8
#45: Protein 50S RIBOSOMAL PROTEIN L13


Mass: 15927.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60488
#46: Protein 50S RIBOSOMAL PROTEIN L14


Mass: 13323.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP8
#47: Protein 50S RIBOSOMAL PROTEIN L15


Mass: 16319.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ7
#48: Protein 50S RIBOSOMAL PROTEIN L16


Mass: 15993.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60489
#49: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q9Z9H5
#50: Protein 50S RIBOSOMAL PROTEIN L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHQ4
#51: Protein 50S RIBOSOMAL PROTEIN L19


Mass: 17188.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60490
#52: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13779.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60491
#53: Protein 50S RIBOSOMAL PROTEIN L21


Mass: 11069.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: P60492
#54: 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) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP3
#55: Protein 50S RIBOSOMAL PROTEIN L23 / L*23


Mass: 10759.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP0
#56: Protein 50S RIBOSOMAL PROTEIN L24


Mass: 12085.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHP9
#57: Protein 50S RIBOSOMAL PROTEIN L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Variant: MRC-MSAW1 / Strain: HB8 / References: UniProt: Q5SHZ1

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Protein / Non-polymers , 2 types, 2 molecules AY

#24: Protein PEPTIDE CHAIN RELEASE FACTOR 3 / RELEASE FACTOR 3 / RF-3


Mass: 59651.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: DH10B / Strain: K-12 / References: UniProt: B1XFI4
#58: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Details

Has protein modificationY
Sequence detailsAUTHOR REQUESTED CHANGE IN RESIDUE NUMBERING FOR CHAIN V ON 23-SEP-2011 AFTER THE RELEASE DEADLINE. ...AUTHOR REQUESTED CHANGE IN RESIDUE NUMBERING FOR CHAIN V ON 23-SEP-2011 AFTER THE RELEASE DEADLINE. THIS CHANGE WAS MADE AS A PART OF A REVDAT ON 30-MAY-2012.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.87 % / Description: NONE
Crystal growpH: 6.7
Details: 100 MM MES-KOH PH 6.7, 20 MM KCL, 7.4% (W/V) PEG20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2011 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→45 Å / Num. obs: 274830 / % possible obs: 99 % / Observed criterion σ(I): 1.3 / Redundancy: 7.44 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.42
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 7.29 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.06 / % possible all: 99

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Processing

Software
NameVersionClassification
CNSmodel building
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J00

2j00
PDB Unreleased entry


Resolution: 3.8→44.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000101 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE IS A LIGAND GDPCP IN THE COORDINATE IN THIS ENTRY. DUE TO THE RELATIVE WEAKER DENSITY OF THE RELEASE FACTOR 3 COMPARED TO THE RIBOSOME, THE CONFORMATION OF THE SIDE CHAINS OF RF3, AND ...Details: THERE IS A LIGAND GDPCP IN THE COORDINATE IN THIS ENTRY. DUE TO THE RELATIVE WEAKER DENSITY OF THE RELEASE FACTOR 3 COMPARED TO THE RIBOSOME, THE CONFORMATION OF THE SIDE CHAINS OF RF3, AND OF THE PRECISE REGISTRY IN REGIONS THAT HAD MOVED RELATIVE TO THE ISOLATED CRYSTAL STRUCTURE (PDB CODE: 2H5E) CAN NOT BE CERTAIN. IONS SUCH AS MG2+ AND WATER MOLECULES WERE NOT FITTED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.351 5622 2 %RANDOM
Rwork0.293 ---
obs0.293 274819 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 7.66545 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 147 Å2
Baniso -1Baniso -2Baniso -3
1--24.15 Å20 Å2-13.13 Å2
2--31.81 Å20 Å2
3----7.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.83 Å0.74 Å
Luzzati d res low-5 Å
Luzzati sigma a1.48 Å1.42 Å
Refinement stepCycle: LAST / Resolution: 3.8→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23091 34161 32 0 57284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 956 2.1 %
Rwork0.425 44893 -
obs--99.2 %

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