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- PDB-4v85: Crystal Structure of Release Factor RF3 Trapped in the GTP State ... -

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Basic information

Entry
Database: PDB / ID: 4v85
TitleCrystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S ribosomal RNA
  • Peptide chain release factor 3
  • Viomycin
  • messenger RNA
KeywordsRIBOSOME/ANTIBIOTIC / typeII release factor binding with ribosome / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of DNA-templated transcription elongation / ribosome assembly / transcription elongation factor complex / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / GDP binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / transferase activity / ribosome binding / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / GTP binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / 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 L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain ...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 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 / : / : / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / 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 L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L6, 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 S4, bacterial-type / Ribosomal protein L5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature.
Similarity search - Domain/homology
Viomycin / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 ...Viomycin / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / 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 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Peptide chain release factor RF3 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZhou, J. / Lancaster, L. / Trakhanov, S. / Noller, H.F.
CitationJournal: Rna / Year: 2012
Title: Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.
Authors: Zhou, J. / Lancaster, L. / Trakhanov, S. / Noller, H.F.
History
DepositionJun 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3SFS, 3SGF
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 11, 2018Group: Advisory / Data collection / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 1
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 1
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15 1
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 S21
AV: messenger RNA
AW: Peptide chain release factor 3
AY: Viomycin
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B4: 50S ribosomal protein L32
B5: 50S ribosomal protein L33
B6: 50S ribosomal protein L34
B7: 50S ribosomal protein L35
B8: 50S ribosomal protein L36 1
BA: 23S rRNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L10
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L7/L12
BK: 50S ribosomal protein L7/L12
BL: 50S ribosomal protein L7/L12
BM: 50S ribosomal protein L7/L12
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 1
BZ: 50S ribosomal protein L25 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,274,150553
Polymers2,261,64659
Non-polymers12,505494
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)257.600, 312.900, 328.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 4 types, 4 molecules AAAVBABB

#1: RNA chain 16S rRNA


Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / References: GenBank: 323376397
#22: RNA chain messenger RNA


Mass: 8862.456 Da / Num. of mol.: 1 / Source method: obtained synthetically
#34: RNA chain 23S rRNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: GenBank: 315134697
#35: RNA chain 5S ribosomal RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: GenBank: 323376397

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

#2: Protein 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3TPN2, UniProt: P0A7V0*PLUS
#3: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQX2, UniProt: P0A7V3*PLUS
#4: Protein 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR62, UniProt: P0A7V8*PLUS
#5: Protein 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR27, UniProt: P0A7W1*PLUS
#6: Protein 30S ribosomal protein S6 1


Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SFQ7, UniProt: P02358*PLUS
#7: Protein 30S ribosomal protein S7


Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQS2, UniProt: P02359*PLUS
#8: Protein 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR12, UniProt: P0A7W7*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SRY2, UniProt: P0A7X3*PLUS
#10: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQT7, UniProt: P0A7R5*PLUS
#11: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR57, UniProt: P0A7R9*PLUS
#12: Protein 30S ribosomal protein S12 1


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQR7, UniProt: P0A7S3*PLUS
#13: Protein 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR52, UniProt: P0A7S9*PLUS
#14: Protein 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR07, UniProt: P0AG59*PLUS
#15: Protein 30S ribosomal protein S15 1


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SSQ7, UniProt: P0ADZ4*PLUS
#16: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SYP2, UniProt: P0A7T3*PLUS
#17: Protein 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQY7, UniProt: P0AG63*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SFP7, UniProt: P0A7T7*PLUS
#19: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQW2, UniProt: P0A7U3*PLUS
#20: Protein 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3STZ7, UniProt: P68679*PLUS

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50S ribosomal protein ... , 30 types, 33 molecules B0B1B2B3B4B5B6B7B8BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBW...

#25: Protein 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SSG7, UniProt: P0A7L8*PLUS
#26: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SME2, UniProt: P0A7M2*PLUS
#27: Protein 50S ribosomal protein L29 / 50S ribosomal subunit protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQY2, UniProt: P0A7M6*PLUS
#28: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR32, UniProt: P0AG51*PLUS
#29: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3TE02, UniProt: P0A7N4*PLUS
#30: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SME7, UniProt: P0A7N9*PLUS
#31: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SLL2, UniProt: P0A7P5*PLUS
#32: Protein 50S ribosomal protein L35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3T7Q2, UniProt: P0A7Q1*PLUS
#33: Protein/peptide 50S ribosomal protein L36 1


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR47, UniProt: P0A7Q6*PLUS
#36: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQV7, UniProt: P60422*PLUS
#37: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQU2, UniProt: P60438*PLUS
#38: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQU7, UniProt: P60723*PLUS
#39: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR02, UniProt: P62399*PLUS
#40: Protein 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR17, UniProt: P0AG55*PLUS
#41: Protein 50S ribosomal protein L10


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SIB7, UniProt: P0A7J3*PLUS
#42: Protein 50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SIC7, UniProt: P0A7J7*PLUS
#43: Protein
50S ribosomal protein L7/L12


Mass: 12309.155 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SIB2, UniProt: P0A7K2*PLUS
#44: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SRX7, UniProt: P0AA10*PLUS
#45: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQZ2, UniProt: P0ADY3*PLUS
#46: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR37, UniProt: P02413*PLUS
#47: Protein 50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQX7, UniProt: P0ADY7*PLUS
#48: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR72, UniProt: P0AG44*PLUS
#49: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SR22, UniProt: P0C018*PLUS
#50: Protein 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SYQ7, UniProt: P0A7K6*PLUS
#51: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3T7Q7, UniProt: P0A7L3*PLUS
#52: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SSG2, UniProt: P0AG48*PLUS
#53: Protein 50S ribosomal protein L22


Mass: 13082.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQW7, UniProt: P61175*PLUS
#54: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQV2, UniProt: P0ADZ0*PLUS
#55: Protein 50S ribosomal protein L24 1


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3SQZ7, UniProt: P60624*PLUS
#56: Protein 50S ribosomal protein L25 1


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CSH142 / References: UniProt: C3T3H7, UniProt: P68919*PLUS

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Protein / Protein/peptide , 2 types, 2 molecules AWAY

#23: Protein Peptide chain release factor 3 / RF-3


Mass: 59651.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600
Gene: b4375, JW5873, miaD, prfC, Termination Release Factor 3, tos
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7I4
#24: Protein/peptide Viomycin


Type: Oligopeptide / Class: Antibiotic / Mass: 703.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces (bacteria) / References: NOR: NOR00633, Viomycin

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Non-polymers , 3 types, 511 molecules

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


Mass: 24.305 Da / Num. of mol.: 493 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 4

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris Ac PH.7.0, 25-35 mM KCL, 6.1% PEG 20000, 1% glycerol, 50mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 433307 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASERphasing
CNS1.2refinement
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→40 Å / σ(F): 1.99 / σ(I): 1.71 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 23871 RANDOM
Rwork0.21 --
obs0.22 433307 -
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22735 33002 137 2 55876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.89
X-RAY DIFFRACTIONf_bond_d0.06

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