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- PDB-4v9p: Control of ribosomal subunit rotation by elongation factor G -

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Basic information

Entry
Database: PDB / ID: 4v9p
TitleControl of ribosomal subunit rotation by elongation factor G
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Viomycin
  • elongation factor G
Keywordsribosome/antibiotic / Protein biosynthesis / ribosome / RNA / EF-G / elongation / factor / GTP / GDPCP / viomycin / tRNA / tranlocation / exit / peptidyl / 50S / 70S / 23S / ribosomal subunit / ribosome-antibiotic complex
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity ...ribosome disassembly / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / 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 / regulation of mRNA stability / negative regulation of translational initiation / 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 / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / ribosome binding / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L10 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / 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 S16, conserved site / Ribosomal protein S16 signature. / 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 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 protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / 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 L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / 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 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
Similarity search - Domain/homology
Viomycin / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 ...Viomycin / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Elongation factor G / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / 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 / Large ribosomal subunit protein bL9 / 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 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsPulk, A. / Cate, J.H.D.
CitationJournal: Science / Year: 2013
Title: Control of ribosomal subunit rotation by elongation factor G.
Authors: Pulk, A. / Cate, J.H.
History
DepositionMay 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4KJ5, 4KJ6, 4KJ7, 4KJ8, 4KJ9, 4KJA, 4KJB, 4KJC
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Source and taxonomy / Structure summary
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...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 / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 23S rRNA
AB: 5S rRNA
AC: 50S ribosomal protein L2
AD: 50S ribosomal protein L3
AE: 50S ribosomal protein L4
AF: 50S ribosomal protein L5
AG: 50S ribosomal protein L6
AH: 50S ribosomal protein L9
AI: 50S ribosomal protein L11
AJ: 50S ribosomal protein L13
AK: 50S ribosomal protein L14
AL: 50S ribosomal protein L15
AM: 50S ribosomal protein L16
AN: 50S ribosomal protein L17
AO: 50S ribosomal protein L18
AP: 50S ribosomal protein L19
AQ: 50S ribosomal protein L20
AR: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
AW: 50S ribosomal protein L27
AX: 50S ribosomal protein L28
AY: 50S ribosomal protein L29
AZ: 50S ribosomal protein L30
A0: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A2: 50S ribosomal protein L34
A3: 50S ribosomal protein L35
A4: 50S ribosomal protein L36
A5: 50S ribosomal protein L10
BA: 16S rRNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein S21
BV: elongation factor G
BW: Viomycin
CA: 23S rRNA
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
CI: 50S ribosomal protein L11
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C0: 50S ribosomal protein L32
C1: 50S ribosomal protein L33
C2: 50S ribosomal protein L34
C3: 50S ribosomal protein L35
C4: 50S ribosomal protein L36
DA: 16S rRNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein S21
DV: elongation factor G
DW: Viomycin
EA: 23S rRNA
EB: 5S rRNA
EC: 50S ribosomal protein L2
ED: 50S ribosomal protein L3
EE: 50S ribosomal protein L4
EF: 50S ribosomal protein L5
EG: 50S ribosomal protein L6
EH: 50S ribosomal protein L9
EI: 50S ribosomal protein L11
EJ: 50S ribosomal protein L13
EK: 50S ribosomal protein L14
EL: 50S ribosomal protein L15
EM: 50S ribosomal protein L16
EN: 50S ribosomal protein L17
EO: 50S ribosomal protein L18
EP: 50S ribosomal protein L19
EQ: 50S ribosomal protein L20
ER: 50S ribosomal protein L21
ES: 50S ribosomal protein L22
ET: 50S ribosomal protein L23
EU: 50S ribosomal protein L24
EV: 50S ribosomal protein L25
EW: 50S ribosomal protein L27
EX: 50S ribosomal protein L28
EY: 50S ribosomal protein L29
EZ: 50S ribosomal protein L30
E0: 50S ribosomal protein L32
E1: 50S ribosomal protein L33
E2: 50S ribosomal protein L34
E3: 50S ribosomal protein L35
E4: 50S ribosomal protein L36
E5: 50S ribosomal protein L10
FA: 16S rRNA
FB: 30S ribosomal protein S2
FC: 30S ribosomal protein S3
FD: 30S ribosomal protein S4
FE: 30S ribosomal protein S5
FF: 30S ribosomal protein S6
FG: 30S ribosomal protein S7
FH: 30S ribosomal protein S8
FI: 30S ribosomal protein S9
FJ: 30S ribosomal protein S10
FK: 30S ribosomal protein S11
FL: 30S ribosomal protein S12
FM: 30S ribosomal protein S13
FN: 30S ribosomal protein S14
FO: 30S ribosomal protein S15
FP: 30S ribosomal protein S16
FQ: 30S ribosomal protein S17
FR: 30S ribosomal protein S18
FS: 30S ribosomal protein S19
FT: 30S ribosomal protein S20
FU: 30S ribosomal protein S21
FV: elongation factor G
FW: Viomycin
GA: 23S rRNA
GB: 5S rRNA
GC: 50S ribosomal protein L2
GD: 50S ribosomal protein L3
GE: 50S ribosomal protein L4
GF: 50S ribosomal protein L5
GG: 50S ribosomal protein L6
GH: 50S ribosomal protein L9
GI: 50S ribosomal protein L11
GJ: 50S ribosomal protein L13
GK: 50S ribosomal protein L14
GL: 50S ribosomal protein L15
GM: 50S ribosomal protein L16
GN: 50S ribosomal protein L17
GO: 50S ribosomal protein L18
GP: 50S ribosomal protein L19
GQ: 50S ribosomal protein L20
GR: 50S ribosomal protein L21
GS: 50S ribosomal protein L22
GT: 50S ribosomal protein L23
GU: 50S ribosomal protein L24
GV: 50S ribosomal protein L25
GW: 50S ribosomal protein L27
GX: 50S ribosomal protein L28
GY: 50S ribosomal protein L29
GZ: 50S ribosomal protein L30
G0: 50S ribosomal protein L32
G1: 50S ribosomal protein L33
G2: 50S ribosomal protein L34
G3: 50S ribosomal protein L35
G4: 50S ribosomal protein L36
HA: 16S rRNA
HB: 30S ribosomal protein S2
HC: 30S ribosomal protein S3
HD: 30S ribosomal protein S4
HE: 30S ribosomal protein S5
HF: 30S ribosomal protein S6
HG: 30S ribosomal protein S7
HH: 30S ribosomal protein S8
HI: 30S ribosomal protein S9
HJ: 30S ribosomal protein S10
HK: 30S ribosomal protein S11
HL: 30S ribosomal protein S12
HM: 30S ribosomal protein S13
HN: 30S ribosomal protein S14
HO: 30S ribosomal protein S15
HP: 30S ribosomal protein S16
HQ: 30S ribosomal protein S17
HR: 30S ribosomal protein S18
HS: 30S ribosomal protein S19
HT: 30S ribosomal protein S20
HU: 30S ribosomal protein S21
HV: elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,915,595965
Polymers8,895,263217
Non-polymers20,332748
Water62,6203476
1
AA: 23S rRNA
AB: 5S rRNA
AC: 50S ribosomal protein L2
AD: 50S ribosomal protein L3
AE: 50S ribosomal protein L4
AF: 50S ribosomal protein L5
AG: 50S ribosomal protein L6
AH: 50S ribosomal protein L9
AI: 50S ribosomal protein L11
AJ: 50S ribosomal protein L13
AK: 50S ribosomal protein L14
AL: 50S ribosomal protein L15
AM: 50S ribosomal protein L16
AN: 50S ribosomal protein L17
AO: 50S ribosomal protein L18
AP: 50S ribosomal protein L19
AQ: 50S ribosomal protein L20
AR: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
AW: 50S ribosomal protein L27
AX: 50S ribosomal protein L28
AY: 50S ribosomal protein L29
AZ: 50S ribosomal protein L30
A0: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A2: 50S ribosomal protein L34
A3: 50S ribosomal protein L35
A4: 50S ribosomal protein L36
A5: 50S ribosomal protein L10
BA: 16S rRNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein S21
BV: elongation factor G
BW: Viomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,237,943242
Polymers2,232,86055
Non-polymers5,083187
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 23S rRNA
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
CI: 50S ribosomal protein L11
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C0: 50S ribosomal protein L32
C1: 50S ribosomal protein L33
C2: 50S ribosomal protein L34
C3: 50S ribosomal protein L35
C4: 50S ribosomal protein L36
DA: 16S rRNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein S21
DV: elongation factor G
DW: Viomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,220,206241
Polymers2,215,12354
Non-polymers5,083187
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
EA: 23S rRNA
EB: 5S rRNA
EC: 50S ribosomal protein L2
ED: 50S ribosomal protein L3
EE: 50S ribosomal protein L4
EF: 50S ribosomal protein L5
EG: 50S ribosomal protein L6
EH: 50S ribosomal protein L9
EI: 50S ribosomal protein L11
EJ: 50S ribosomal protein L13
EK: 50S ribosomal protein L14
EL: 50S ribosomal protein L15
EM: 50S ribosomal protein L16
EN: 50S ribosomal protein L17
EO: 50S ribosomal protein L18
EP: 50S ribosomal protein L19
EQ: 50S ribosomal protein L20
ER: 50S ribosomal protein L21
ES: 50S ribosomal protein L22
ET: 50S ribosomal protein L23
EU: 50S ribosomal protein L24
EV: 50S ribosomal protein L25
EW: 50S ribosomal protein L27
EX: 50S ribosomal protein L28
EY: 50S ribosomal protein L29
EZ: 50S ribosomal protein L30
E0: 50S ribosomal protein L32
E1: 50S ribosomal protein L33
E2: 50S ribosomal protein L34
E3: 50S ribosomal protein L35
E4: 50S ribosomal protein L36
E5: 50S ribosomal protein L10
FA: 16S rRNA
FB: 30S ribosomal protein S2
FC: 30S ribosomal protein S3
FD: 30S ribosomal protein S4
FE: 30S ribosomal protein S5
FF: 30S ribosomal protein S6
FG: 30S ribosomal protein S7
FH: 30S ribosomal protein S8
FI: 30S ribosomal protein S9
FJ: 30S ribosomal protein S10
FK: 30S ribosomal protein S11
FL: 30S ribosomal protein S12
FM: 30S ribosomal protein S13
FN: 30S ribosomal protein S14
FO: 30S ribosomal protein S15
FP: 30S ribosomal protein S16
FQ: 30S ribosomal protein S17
FR: 30S ribosomal protein S18
FS: 30S ribosomal protein S19
FT: 30S ribosomal protein S20
FU: 30S ribosomal protein S21
FV: elongation factor G
FW: Viomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,237,943242
Polymers2,232,86055
Non-polymers5,083187
Water34219
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GA: 23S rRNA
GB: 5S rRNA
GC: 50S ribosomal protein L2
GD: 50S ribosomal protein L3
GE: 50S ribosomal protein L4
GF: 50S ribosomal protein L5
GG: 50S ribosomal protein L6
GH: 50S ribosomal protein L9
GI: 50S ribosomal protein L11
GJ: 50S ribosomal protein L13
GK: 50S ribosomal protein L14
GL: 50S ribosomal protein L15
GM: 50S ribosomal protein L16
GN: 50S ribosomal protein L17
GO: 50S ribosomal protein L18
GP: 50S ribosomal protein L19
GQ: 50S ribosomal protein L20
GR: 50S ribosomal protein L21
GS: 50S ribosomal protein L22
GT: 50S ribosomal protein L23
GU: 50S ribosomal protein L24
GV: 50S ribosomal protein L25
GW: 50S ribosomal protein L27
GX: 50S ribosomal protein L28
GY: 50S ribosomal protein L29
GZ: 50S ribosomal protein L30
G0: 50S ribosomal protein L32
G1: 50S ribosomal protein L33
G2: 50S ribosomal protein L34
G3: 50S ribosomal protein L35
G4: 50S ribosomal protein L36
HA: 16S rRNA
HB: 30S ribosomal protein S2
HC: 30S ribosomal protein S3
HD: 30S ribosomal protein S4
HE: 30S ribosomal protein S5
HF: 30S ribosomal protein S6
HG: 30S ribosomal protein S7
HH: 30S ribosomal protein S8
HI: 30S ribosomal protein S9
HJ: 30S ribosomal protein S10
HK: 30S ribosomal protein S11
HL: 30S ribosomal protein S12
HM: 30S ribosomal protein S13
HN: 30S ribosomal protein S14
HO: 30S ribosomal protein S15
HP: 30S ribosomal protein S16
HQ: 30S ribosomal protein S17
HR: 30S ribosomal protein S18
HS: 30S ribosomal protein S19
HT: 30S ribosomal protein S20
HU: 30S ribosomal protein S21
HV: elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,219,503240
Polymers2,214,42053
Non-polymers5,083187
Water41423
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)361.14, 360.51, 429.73
Angle α, β, γ (deg.)90, 103.217, 90
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 3 types, 12 molecules AACAEAGAABCBEBGBBADAFAHA

#1: RNA chain
23S rRNA


Mass: 941612.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306.1
#2: RNA chain
5S rRNA


Mass: 38790.090 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306.1
#33: RNA chain
16S rRNA


Mass: 499690.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: GenBank: AP012306.1

+
50S ribosomal protein ... , 30 types, 118 molecules ACCCECGCADCDEDGDAECEEEGEAFCFEFGFAGCGEGGGAHCHEHGHAICIEIGIAJCJ...

#3: Protein
50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60422
#4: Protein
50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60438
#5: Protein
50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60723
#6: Protein
50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P62399
#7: Protein
50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG55
#8: Protein/peptide
50S ribosomal protein L9


Mass: 5467.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: truncated C-terminal domain expressing peptide 1-50 residues
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: rpll / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1
#9: Protein
50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7J7
#10: Protein
50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AA10
#11: Protein
50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADY3
#12: Protein
50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P02413
#13: Protein
50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADY7
#14: Protein
50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG44
#15: Protein
50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0C018
#16: Protein
50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7K6
#17: Protein
50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7L3
#18: Protein
50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG48
#19: Protein
50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P61175
#20: Protein
50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADZ0
#21: Protein
50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60624
#22: Protein
50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P68919
#23: Protein
50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7L8
#24: Protein
50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7M2
#25: Protein
50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7M6
#26: Protein
50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG51
#27: Protein
50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7N4
#28: Protein
50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7N9
#29: Protein/peptide
50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7P5
#30: Protein
50S ribosomal protein L35


Mass: 7313.032 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7Q1
#31: Protein/peptide
50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7Q6
#32: Protein 50S ribosomal protein L10


Mass: 17736.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7J3

-
30S ribosomal protein ... , 20 types, 80 molecules BBDBFBHBBCDCFCHCBDDDFDHDBEDEFEHEBFDFFFHFBGDGFGHGBHDHFHHHBIDI...

#34: Protein
30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V0
#35: Protein
30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V3
#36: Protein
30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V8
#37: Protein
30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7W1
#38: Protein
30S ribosomal protein S6


Mass: 15727.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P02358
#39: Protein
30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P02359
#40: Protein
30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7W7
#41: Protein
30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7X3
#42: Protein
30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7R5
#43: Protein
30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7R9
#44: Protein
30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7S3
#45: Protein
30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7S9
#46: Protein
30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0AG59
#47: Protein
30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0ADZ4
#48: Protein
30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7T3
#49: Protein
30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0AG63
#50: Protein
30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7T7
#51: Protein
30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7U3
#52: Protein
30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7U7
#53: Protein
30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P68679

-
Protein / Protein/peptide , 2 types, 7 molecules BVDVFVHVBWDWFW

#54: Protein
elongation factor G


Mass: 77676.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: fusA / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6M8
#55: Protein/peptide Viomycin


Type: Oligopeptide / Class: Antibiotic / Mass: 703.707 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Streptomyces (bacteria) / References: NOR: NOR00633, Viomycin

-
Non-polymers , 4 types, 4224 molecules

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


Mass: 24.305 Da / Num. of mol.: 740 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#58: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3476 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 24

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0659.82
2
3
4
5
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911microbatch6.5PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
2912microbatch6.5PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
2913microbatch6.5PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
2914microbatch6.5PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
2915microbatch6.5PEG8k, KSCN, pH 6.5, microbatch, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.1
SYNCHROTRONALS 12.3.121.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 3, 2012
ADSC QUANTUM 3152CCDNov 16, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→70 Å / Num. obs: 1984536 / % possible obs: 89.6 % / Observed criterion σ(F): 0.58 / Observed criterion σ(I): 0.58

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→70 Å / Occupancy max: 1 / Occupancy min: 0.89 / σ(F): 0.58
Details: Zero B values occur for some waters due to scaling from the use of bulk solvent correction in the refinement
RfactorNum. reflection
Rfree0.2671 8583
Rwork0.2146 -
all-2353155
obs-1984536
Displacement parametersBiso max: 145.92 Å2 / Biso mean: 32.7421 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26525 63803 142 660 91130

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