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- PDB-6b4v: Antibiotic blasticidin S and E. coli release factor 1 bound to th... -

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Basic information

Entry
Database: PDB / ID: 6b4v
TitleAntibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Peptide chain release factor 1
  • mRNA
  • tRNA
KeywordsRIBOSOME/ANTIBIOTIC / termination suppression / class I release factors / RF1 / stop-codon recognition / termination / blasticidin S / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small 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
Peptide chain release factor 1 / : / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx ...Peptide chain release factor 1 / : / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like
Similarity search - Domain/homology
BLASTICIDIN S / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Peptide chain release factor 1 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX ...BLASTICIDIN S / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Peptide chain release factor 1 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / 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 bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
Escherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSvidritskiy, E. / Korostelev, A.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK047757 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Mechanism of Inhibition of Translation Termination by Blasticidin S.
Authors: Svidritskiy, E. / Korostelev, A.A.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 19, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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 / refine_hist / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Mar 19, 2025Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 23S ribosomal RNA
C: 5S ribosomal RNA
D: tRNA
E: 50S ribosomal protein L2
F: 50S ribosomal protein L3
G: 50S ribosomal protein L4
H: 50S ribosomal protein L5
I: 50S ribosomal protein L6
J: 50S ribosomal protein L9
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
AA: 50S ribosomal protein L30
BA: 50S ribosomal protein L31
CA: 50S ribosomal protein L32
DA: 50S ribosomal protein L33
EA: 50S ribosomal protein L34
FA: 50S ribosomal protein L35
GA: 50S ribosomal protein L36
HA: mRNA
IA: tRNA
JA: Peptide chain release factor 1
KA: 30S ribosomal protein S2
LA: 30S ribosomal protein S3
MA: 30S ribosomal protein S4
NA: 30S ribosomal protein S5
OA: 30S ribosomal protein S6
PA: 30S ribosomal protein S7
QA: 30S ribosomal protein S8
RA: 30S ribosomal protein S9
SA: 30S ribosomal protein S10
TA: 30S ribosomal protein S11
UA: 30S ribosomal protein S12
VA: 30S ribosomal protein S13
WA: 30S ribosomal protein S14 type Z
XA: 30S ribosomal protein S15
YA: 30S ribosomal protein S16
ZA: 30S ribosomal protein S17
AB: 30S ribosomal protein S18
BB: 30S ribosomal protein S19
CB: 30S ribosomal protein S20
DB: 30S ribosomal protein Thx
EB: 16S ribosomal RNA
FB: 23S ribosomal RNA
GB: 5S ribosomal RNA
HB: tRNA
IB: 50S ribosomal protein L2
JB: 50S ribosomal protein L3
KB: 50S ribosomal protein L4
LB: 50S ribosomal protein L5
MB: 50S ribosomal protein L6
NB: 50S ribosomal protein L9
OB: 50S ribosomal protein L13
PB: 50S ribosomal protein L14
QB: 50S ribosomal protein L15
RB: 50S ribosomal protein L16
SB: 50S ribosomal protein L17
TB: 50S ribosomal protein L18
UB: 50S ribosomal protein L19
VB: 50S ribosomal protein L20
WB: 50S ribosomal protein L21
XB: 50S ribosomal protein L22
YB: 50S ribosomal protein L23
ZB: 50S ribosomal protein L24
AC: 50S ribosomal protein L25
BC: 50S ribosomal protein L27
CC: 50S ribosomal protein L28
DC: 50S ribosomal protein L29
EC: 50S ribosomal protein L30
FC: 50S ribosomal protein L31
GC: 50S ribosomal protein L32
HC: 50S ribosomal protein L33
IC: 50S ribosomal protein L34
JC: 50S ribosomal protein L35
KC: 50S ribosomal protein L36
LC: mRNA
MC: tRNA
NC: Peptide chain release factor 1
OC: 30S ribosomal protein S2
PC: 30S ribosomal protein S3
QC: 30S ribosomal protein S4
RC: 30S ribosomal protein S5
SC: 30S ribosomal protein S6
TC: 30S ribosomal protein S7
UC: 30S ribosomal protein S8
VC: 30S ribosomal protein S9
WC: 30S ribosomal protein S10
XC: 30S ribosomal protein S11
YC: 30S ribosomal protein S12
ZC: 30S ribosomal protein S13
AD: 30S ribosomal protein S14 type Z
BD: 30S ribosomal protein S15
CD: 30S ribosomal protein S16
DD: 30S ribosomal protein S17
ED: 30S ribosomal protein S18
FD: 30S ribosomal protein S19
GD: 30S ribosomal protein S20
HD: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,544,2661807
Polymers4,501,862112
Non-polymers42,4041695
Water00
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A: 16S ribosomal RNA
B: 23S ribosomal RNA
C: 5S ribosomal RNA
D: tRNA
E: 50S ribosomal protein L2
F: 50S ribosomal protein L3
G: 50S ribosomal protein L4
H: 50S ribosomal protein L5
I: 50S ribosomal protein L6
J: 50S ribosomal protein L9
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
AA: 50S ribosomal protein L30
BA: 50S ribosomal protein L31
CA: 50S ribosomal protein L32
DA: 50S ribosomal protein L33
EA: 50S ribosomal protein L34
FA: 50S ribosomal protein L35
GA: 50S ribosomal protein L36
HA: mRNA
IA: tRNA
JA: Peptide chain release factor 1
KA: 30S ribosomal protein S2
LA: 30S ribosomal protein S3
MA: 30S ribosomal protein S4
NA: 30S ribosomal protein S5
OA: 30S ribosomal protein S6
PA: 30S ribosomal protein S7
QA: 30S ribosomal protein S8
RA: 30S ribosomal protein S9
SA: 30S ribosomal protein S10
TA: 30S ribosomal protein S11
UA: 30S ribosomal protein S12
VA: 30S ribosomal protein S13
WA: 30S ribosomal protein S14 type Z
XA: 30S ribosomal protein S15
YA: 30S ribosomal protein S16
ZA: 30S ribosomal protein S17
AB: 30S ribosomal protein S18
BB: 30S ribosomal protein S19
CB: 30S ribosomal protein S20
DB: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,273,458958
Polymers2,250,93156
Non-polymers22,527902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
EB: 16S ribosomal RNA
FB: 23S ribosomal RNA
GB: 5S ribosomal RNA
HB: tRNA
IB: 50S ribosomal protein L2
JB: 50S ribosomal protein L3
KB: 50S ribosomal protein L4
LB: 50S ribosomal protein L5
MB: 50S ribosomal protein L6
NB: 50S ribosomal protein L9
OB: 50S ribosomal protein L13
PB: 50S ribosomal protein L14
QB: 50S ribosomal protein L15
RB: 50S ribosomal protein L16
SB: 50S ribosomal protein L17
TB: 50S ribosomal protein L18
UB: 50S ribosomal protein L19
VB: 50S ribosomal protein L20
WB: 50S ribosomal protein L21
XB: 50S ribosomal protein L22
YB: 50S ribosomal protein L23
ZB: 50S ribosomal protein L24
AC: 50S ribosomal protein L25
BC: 50S ribosomal protein L27
CC: 50S ribosomal protein L28
DC: 50S ribosomal protein L29
EC: 50S ribosomal protein L30
FC: 50S ribosomal protein L31
GC: 50S ribosomal protein L32
HC: 50S ribosomal protein L33
IC: 50S ribosomal protein L34
JC: 50S ribosomal protein L35
KC: 50S ribosomal protein L36
LC: mRNA
MC: tRNA
NC: Peptide chain release factor 1
OC: 30S ribosomal protein S2
PC: 30S ribosomal protein S3
QC: 30S ribosomal protein S4
RC: 30S ribosomal protein S5
SC: 30S ribosomal protein S6
TC: 30S ribosomal protein S7
UC: 30S ribosomal protein S8
VC: 30S ribosomal protein S9
WC: 30S ribosomal protein S10
XC: 30S ribosomal protein S11
YC: 30S ribosomal protein S12
ZC: 30S ribosomal protein S13
AD: 30S ribosomal protein S14 type Z
BD: 30S ribosomal protein S15
CD: 30S ribosomal protein S16
DD: 30S ribosomal protein S17
ED: 30S ribosomal protein S18
FD: 30S ribosomal protein S19
GD: 30S ribosomal protein S20
HD: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,270,809849
Polymers2,250,93156
Non-polymers19,878793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.849, 452.539, 624.45
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain , 5 types, 12 molecules AEBBFBCGBDIAHBMCHALC

#1: RNA chain 16S ribosomal RNA


Mass: 489561.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#2: RNA chain 23S ribosomal RNA


Mass: 936785.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#3: RNA chain 5S ribosomal RNA


Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#4: RNA chain
tRNA


Mass: 24846.902 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#34: RNA chain mRNA


Mass: 7545.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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50S ribosomal protein ... , 29 types, 58 molecules EIBFJBGKBHLBIMBJNBKOBLPBMQBNRBOSBPTBQUBRVBSWB...

#5: Protein 50S ribosomal protein L2


Mass: 30401.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I07
#6: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I04
#7: Protein 50S ribosomal protein L4


Mass: 22744.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I05
#8: Protein 50S ribosomal protein L5


Mass: 21075.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I16
#9: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I19
#10: Protein 50S ribosomal protein L9


Mass: 16436.205 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GV5
#11: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IN1
#12: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I14
#13: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I23
#14: Protein 50S ribosomal protein L16


Mass: 15977.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I11
#15: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I33
#16: Protein 50S ribosomal protein L18


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I20
#17: Protein 50S ribosomal protein L19


Mass: 17217.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JU9
#18: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L76
#19: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72HR2
#20: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I09
#21: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I06
#22: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I15
#23: Protein 50S ribosomal protein L25


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IA7
#24: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72HR3
#25: Protein 50S ribosomal protein L28


Mass: 11032.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72G84
#26: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I12
#27: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I22
#28: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JR0
#29: Protein 50S ribosomal protein L32


Mass: 6734.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62652
#30: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GW3
#31: 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 HB27 (bacteria) / References: UniProt: P80340
#32: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L77
#33: 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 HB27 (bacteria) / References: UniProt: Q72I28

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Protein , 1 types, 2 molecules JANC

#35: Protein Peptide chain release factor 1


Mass: 41644.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A7ZKY5

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30S ribosomal protein ... , 20 types, 40 molecules KAOCLAPCMAQCNARCOASCPATCQAUCRAVCSAWCTAXCUAYCVAZCWAADXABDYACD...

#36: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62662
#37: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62663
#38: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62664
#39: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62665
#40: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62666
#41: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62667
#42: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62668
#43: Protein 30S ribosomal protein S9


Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62669
#44: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62653
#45: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62654
#46: Protein 30S ribosomal protein S12


Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P61941
#47: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62655
#48: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62656
#49: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62657
#50: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62238
#51: Protein 30S ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62658
#52: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62659
#53: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62660
#54: Protein 30S ribosomal protein S20


Mass: 11722.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62661
#55: 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 HB27 (bacteria) / References: UniProt: P62611, UniProt: P62613*PLUS

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Non-polymers , 3 types, 1695 molecules

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


Mass: 24.305 Da / Num. of mol.: 1683 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-BLS / BLASTICIDIN S


Mass: 422.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N8O5 / Comment: antibiotic*YM
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn

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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: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3 uL 70S*mRNA*tRNAfMet*RF1*antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli ...Details: 3 uL 70S*mRNA*tRNAfMet*RF1*antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→70 Å / Num. obs: 813599 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 6.89
Reflection shellHighest resolution: 3.4 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→50 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs813599 99.9 %
Rfree-2 %
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms97078 201010 1753 0 299841

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