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- PDB-4w2i: Crystal structure of the Thermus thermophilus 70S ribosome in com... -

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Basic information

Entry
Database: PDB / ID: 4w2i
TitleCrystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites
Components
  • (30S Ribosomal Protein ...) x 20
  • (50S Ribosomal Protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • A/P-site tRNA
  • E-site tRNA
  • mRNA
KeywordsRIBOSOME/ANTIBIOTIC / Negamycin / antibiotic / 70S ribosome / inhibition of translation / miscoding / translocation inhibitor / 30S subunit with negamycin / mRNA / deacylated A- / P- / and E-site tRNAs of the 1st 70S ribosome in the ASU / Functional complex of bacterial 70S ribosome with antibiotic negamycin / 50S subunit of the 1st 70S ribosome in the ASU / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein S11, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal protein S18, conserved site / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type / Ribosomal L32p protein family
Similarity search - Domain/homology
: / NEGAMYCIN / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 ...: / NEGAMYCIN / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / 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 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPolikanov, Y.S. / Szal, T. / Jiang, F. / Gupta, P. / Matsuda, R. / Shiozuka, M. / Steitz, T.A. / Vazquez-Laslop, N. / Mankin, A.S.
CitationJournal: Mol.Cell / Year: 2014
Title: Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.
Authors: Polikanov, Y.S. / Szal, T. / Jiang, F. / Gupta, P. / Matsuda, R. / Shiozuka, M. / Steitz, T.A. / Vazquez-Laslop, N. / Mankin, A.S.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4RBH, 4RBI, 4RBJ, 4RBK
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_PDB_ins_code / _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_ptnr1_PDB_ins_code / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S Ribosomal RNA
AB: 30S Ribosomal Protein S2
AC: 30S Ribosomal Protein S3
AD: 30S Ribosomal Protein S4
AE: 30S Ribosomal Protein S5
AF: 30S Ribosomal Protein S6
AG: 30S Ribosomal Protein S7
AH: 30S Ribosomal Protein S8
AI: 30S Ribosomal Protein S9
AJ: 30S Ribosomal Protein S10
AK: 30S Ribosomal Protein S11
AL: 30S Ribosomal Protein S12
AM: 30S Ribosomal Protein S13
AN: 30S Ribosomal Protein S14
AO: 30S Ribosomal Protein S15
AP: 30S Ribosomal Protein S16
AQ: 30S Ribosomal Protein S17
AR: 30S Ribosomal Protein S18
AS: 30S Ribosomal Protein S19
AT: 30S Ribosomal Protein S20
AU: 30S Ribosomal Protein THX
AV: mRNA
AW: A/P-site tRNA
AX: E-site tRNA
AY: A/P-site tRNA
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
BD: 50S Ribosomal Protein L2
BE: 50S Ribosomal Protein L3
BF: 50S Ribosomal Protein L4
BG: 50S Ribosomal Protein L5
BH: 50S Ribosomal Protein L6
BI: 50S Ribosomal Protein L9
BN: 50S Ribosomal Protein L13
BO: 50S Ribosomal Protein L14
BP: 50S Ribosomal Protein L15
BQ: 50S Ribosomal Protein L16
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
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
CA: 16S Ribosomal RNA
CB: 30S Ribosomal Protein S2
CC: 30S Ribosomal Protein S3
CD: 30S Ribosomal Protein S4
CE: 30S Ribosomal Protein S5
CF: 30S Ribosomal Protein S6
CG: 30S Ribosomal Protein S7
CH: 30S Ribosomal Protein S8
CI: 30S Ribosomal Protein S9
CJ: 30S Ribosomal Protein S10
CK: 30S Ribosomal Protein S11
CL: 30S Ribosomal Protein S12
CM: 30S Ribosomal Protein S13
CN: 30S Ribosomal Protein S14
CO: 30S Ribosomal Protein S15
CP: 30S Ribosomal Protein S16
CQ: 30S Ribosomal Protein S17
CR: 30S Ribosomal Protein S18
CS: 30S Ribosomal Protein S19
CT: 30S Ribosomal Protein S20
CU: 30S Ribosomal Protein THX
CV: mRNA
CW: A/P-site tRNA
CX: E-site tRNA
CY: A/P-site tRNA
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
DD: 50S Ribosomal Protein L2
DE: 50S Ribosomal Protein L3
DF: 50S Ribosomal Protein L4
DG: 50S Ribosomal Protein L5
DH: 50S Ribosomal Protein L6
DI: 50S Ribosomal Protein L9
DN: 50S Ribosomal Protein L13
DO: 50S Ribosomal Protein L14
DP: 50S Ribosomal Protein L15
DQ: 50S Ribosomal Protein L16
DR: 50S Ribosomal Protein L17
DS: 50S Ribosomal Protein L18
DT: 50S Ribosomal Protein L19
DU: 50S Ribosomal Protein L20
DV: 50S Ribosomal Protein L21
DW: 50S Ribosomal Protein L22
DX: 50S Ribosomal Protein L23
DY: 50S Ribosomal Protein L24
DZ: 50S Ribosomal Protein L25
D0: 50S Ribosomal Protein L27
D1: 50S Ribosomal Protein L28
D2: 50S Ribosomal Protein L29
D3: 50S Ribosomal Protein L30
D4: 50S Ribosomal Protein L31
D5: 50S Ribosomal Protein L32
D6: 50S Ribosomal Protein L33
D7: 50S Ribosomal Protein L34
D8: 50S Ribosomal Protein L35
D9: 50S Ribosomal Protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,555,2882160
Polymers4,500,078112
Non-polymers55,2102048
Water54,9283049
1
AA: 16S Ribosomal RNA
AB: 30S Ribosomal Protein S2
AC: 30S Ribosomal Protein S3
AD: 30S Ribosomal Protein S4
AE: 30S Ribosomal Protein S5
AF: 30S Ribosomal Protein S6
AG: 30S Ribosomal Protein S7
AH: 30S Ribosomal Protein S8
AI: 30S Ribosomal Protein S9
AJ: 30S Ribosomal Protein S10
AK: 30S Ribosomal Protein S11
AL: 30S Ribosomal Protein S12
AM: 30S Ribosomal Protein S13
AN: 30S Ribosomal Protein S14
AO: 30S Ribosomal Protein S15
AP: 30S Ribosomal Protein S16
AQ: 30S Ribosomal Protein S17
AR: 30S Ribosomal Protein S18
AS: 30S Ribosomal Protein S19
AT: 30S Ribosomal Protein S20
AU: 30S Ribosomal Protein THX
AV: mRNA
AW: A/P-site tRNA
AX: E-site tRNA
AY: A/P-site tRNA
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
BD: 50S Ribosomal Protein L2
BE: 50S Ribosomal Protein L3
BF: 50S Ribosomal Protein L4
BG: 50S Ribosomal Protein L5
BH: 50S Ribosomal Protein L6
BI: 50S Ribosomal Protein L9
BN: 50S Ribosomal Protein L13
BO: 50S Ribosomal Protein L14
BP: 50S Ribosomal Protein L15
BQ: 50S Ribosomal Protein L16
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,280,9351220
Polymers2,250,03956
Non-polymers30,8961164
Water61334
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S Ribosomal RNA
CB: 30S Ribosomal Protein S2
CC: 30S Ribosomal Protein S3
CD: 30S Ribosomal Protein S4
CE: 30S Ribosomal Protein S5
CF: 30S Ribosomal Protein S6
CG: 30S Ribosomal Protein S7
CH: 30S Ribosomal Protein S8
CI: 30S Ribosomal Protein S9
CJ: 30S Ribosomal Protein S10
CK: 30S Ribosomal Protein S11
CL: 30S Ribosomal Protein S12
CM: 30S Ribosomal Protein S13
CN: 30S Ribosomal Protein S14
CO: 30S Ribosomal Protein S15
CP: 30S Ribosomal Protein S16
CQ: 30S Ribosomal Protein S17
CR: 30S Ribosomal Protein S18
CS: 30S Ribosomal Protein S19
CT: 30S Ribosomal Protein S20
CU: 30S Ribosomal Protein THX
CV: mRNA
CW: A/P-site tRNA
CX: E-site tRNA
CY: A/P-site tRNA
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
DD: 50S Ribosomal Protein L2
DE: 50S Ribosomal Protein L3
DF: 50S Ribosomal Protein L4
DG: 50S Ribosomal Protein L5
DH: 50S Ribosomal Protein L6
DI: 50S Ribosomal Protein L9
DN: 50S Ribosomal Protein L13
DO: 50S Ribosomal Protein L14
DP: 50S Ribosomal Protein L15
DQ: 50S Ribosomal Protein L16
DR: 50S Ribosomal Protein L17
DS: 50S Ribosomal Protein L18
DT: 50S Ribosomal Protein L19
DU: 50S Ribosomal Protein L20
DV: 50S Ribosomal Protein L21
DW: 50S Ribosomal Protein L22
DX: 50S Ribosomal Protein L23
DY: 50S Ribosomal Protein L24
DZ: 50S Ribosomal Protein L25
D0: 50S Ribosomal Protein L27
D1: 50S Ribosomal Protein L28
D2: 50S Ribosomal Protein L29
D3: 50S Ribosomal Protein L30
D4: 50S Ribosomal Protein L31
D5: 50S Ribosomal Protein L32
D6: 50S Ribosomal Protein L33
D7: 50S Ribosomal Protein L34
D8: 50S Ribosomal Protein L35
D9: 50S Ribosomal Protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,274,353940
Polymers2,250,03956
Non-polymers24,314884
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.250, 443.610, 619.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThis PDB entry contains coordinates for the 30S subunit with negamycin, mRNA, deacylated A-, P-, and E-site tRNAs of the 1st 70S ribosome in the ASU. The full biological assembly can be obtained by combining coordinates from this entry and the entry for the 50S subunit of the 1st 70S ribosome. The entire ASU contains two 70S ribosomes.

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Components

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RNA chain , 6 types, 14 molecules AACAAVCVAWAYCWCYAXCXBADABBDB

#1: RNA chain 16S Ribosomal RNA


Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382
#22: RNA chain mRNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) synthetic construct (others)
#23: RNA chain
A/P-site tRNA


Mass: 24645.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Phenylalanine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600
#24: RNA chain E-site tRNA


Mass: 24846.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Initiator Methionine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600
#25: RNA chain 23S Ribosomal RNA


Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382
#26: RNA chain 5S Ribosomal RNA


Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382

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30S Ribosomal Protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...

#2: Protein 30S Ribosomal Protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S Ribosomal Protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S Ribosomal Protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S Ribosomal Protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S Ribosomal Protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S Ribosomal Protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S Ribosomal Protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: Protein 30S Ribosomal Protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S Ribosomal Protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S Ribosomal Protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S Ribosomal Protein S12


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S Ribosomal Protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S Ribosomal Protein S14


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S Ribosomal Protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S Ribosomal Protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S Ribosomal Protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S Ribosomal Protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S Ribosomal Protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S Ribosomal Protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S Ribosomal Protein THX


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

+
50S Ribosomal Protein ... , 29 types, 58 molecules BDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDUBVDV...

#27: Protein 50S Ribosomal Protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#28: Protein 50S Ribosomal Protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#29: Protein 50S Ribosomal Protein L4


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#30: Protein 50S Ribosomal Protein L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#31: Protein 50S Ribosomal Protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#32: Protein 50S Ribosomal Protein L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#33: Protein 50S Ribosomal Protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#34: Protein 50S Ribosomal Protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#35: Protein 50S Ribosomal Protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#36: Protein 50S Ribosomal Protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#37: Protein 50S Ribosomal Protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#38: Protein 50S Ribosomal Protein L18


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#39: Protein 50S Ribosomal Protein L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#40: Protein 50S Ribosomal Protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#41: Protein 50S Ribosomal Protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#42: Protein 50S Ribosomal Protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#43: Protein 50S Ribosomal Protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#44: Protein 50S Ribosomal Protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#45: Protein 50S Ribosomal Protein L25


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#46: Protein 50S Ribosomal Protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#47: Protein 50S Ribosomal Protein L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#48: Protein 50S Ribosomal Protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#49: Protein 50S Ribosomal Protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#50: Protein 50S Ribosomal Protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#51: Protein 50S Ribosomal Protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#52: Protein 50S Ribosomal Protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#53: Protein/peptide 50S Ribosomal Protein L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#54: Protein 50S Ribosomal Protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#55: Protein/peptide 50S Ribosomal Protein L36


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

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Non-polymers , 6 types, 5097 molecules

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


Mass: 24.305 Da / Num. of mol.: 2013 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-NEG / NEGAMYCIN / 3,6-DIAMINO-1-[2-(CARBOXYMETHYL)-2-METHYLHYDRAZINO]-2,3,4,6-TETRADEOXY-L-THREO-HEXOSE


Mass: 248.279 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C9H20N4O4
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3049 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2013 / Details: S/N 60-0112-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→360.635 Å / Num. all: 1548559 / Num. obs: 1505170 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.504 % / Biso Wilson estimate: 54.16 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.04 / Net I/σ(I): 8.77
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-2.770.2970.993967391140501124431.48198.6
2.77-2.850.4171.323867101111171092061.14998.3
2.85-2.930.5541.753697171080551058530.86698
2.93-3.020.6942.373449061050741020340.62797.1
3.02-3.120.8153.28336917101774999450.4598.2
3.12-3.230.8854.4134889398489971250.34498.6
3.23-3.350.9235.5133333395179934810.27898.2
3.35-3.490.9436.4631604991507891450.23597.4
3.49-3.640.9597.7429543787948851230.19596.8
3.64-3.820.9719.1926323483943807400.15996.2
3.82-4.020.98111.328203580048783560.13297.9
4.02-4.270.9861326474575749736190.11297.2
4.27-4.560.98914.8524429971186685190.09496.3
4.56-4.930.99116.2121306666391629720.08294.9
4.93-5.40.99418.2921126661182593830.0797.1
5.4-6.040.99519.4919536755441536870.06396.8
6.04-6.970.99620.2516604949045464500.05794.7
6.97-8.540.99723.3313616141606395290.04595
8.54-12.070.99827.8411148132443309490.03595.4
12.070.99931.745696218332166110.02790.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→124.249 Å / FOM work R set: 0.8091 / SU ML: 0.44 / σ(F): 1.33 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 75597 5.02 %
Rwork0.2099 --
obs0.2122 1504930 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.11 Å2 / Biso mean: 59.48 Å2 / Biso min: 22.66 Å2
Refinement stepCycle: LAST / Resolution: 2.7→124.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91187 200774 2366 3049 297376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006322080
X-RAY DIFFRACTIONf_angle_d1.026478952
X-RAY DIFFRACTIONf_chiral_restr0.04460421
X-RAY DIFFRACTIONf_plane_restr0.00525501
X-RAY DIFFRACTIONf_dihedral_angle_d16.365148184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.73070.396525000.3567480615056199
2.7307-2.76280.396526020.3532479055050799
2.7628-2.79650.375724900.3264480195050998
2.7965-2.83190.358226190.3144478295044898
2.8319-2.86920.346625640.2992478205038498
2.8692-2.90850.337525610.2869476725023398
2.9085-2.950.338325080.2835477915029998
2.95-2.99410.327225270.2727476085013598
2.9941-3.04090.326725510.2727468454939696
3.0409-3.09070.326525010.2718482015070299
3.0907-3.1440.305224840.2548482875077199
3.144-3.20120.300925270.241482815080899
3.2012-3.26280.284324990.2282481155061498
3.2628-3.32940.273924950.2189479935048898
3.3294-3.40180.274824800.216478465032698
3.4018-3.48090.267925150.2169475255004097
3.4809-3.5680.273925330.2161473984993197
3.568-3.66440.263224830.2083472684975196
3.6644-3.77230.248424740.2467284920295
3.7723-3.8940.245124760.1948480085048498
3.894-4.03320.239525300.1926479885051898
4.0332-4.19470.238825610.1901476625022397
4.1947-4.38560.228624970.1856474344993197
4.3856-4.61690.230525180.1812471844970296
4.6169-4.90610.222724860.1772465504903695
4.9061-5.2850.214625090.169475885009797
5.285-5.81680.210725490.1685479075045697
5.8168-6.65850.220925050.1738471654967095
6.6585-8.38870.216125310.1752470854961695
8.3887-124.38080.213225220.1918475705009294

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