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- PDB-6boh: Antibiotic blasticidin S and E. coli release factor 1 (containing... -

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Basic information

Entry
Database: PDB / ID: 6boh
TitleAntibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Peptide chain release factor 1
  • mRNA
  • tRNA
KeywordsRIBOSOME/ANTIBIOTIC / class I release factors / closed RF1 / stop-codon recognition / termination accuracy / blasticidin S / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / 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 L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein L20 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily
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 / 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 speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
Escherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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: Structure / Year: 2018
Title: Conformational Control of Translation Termination on the 70S Ribosome.
Authors: Svidritskiy, E. / Korostelev, A.A.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: Peptide chain release factor 1
LA: 30S ribosomal protein S2
MA: 30S ribosomal protein S3
NA: 50S ribosomal protein S4
OA: 30S ribosomal protein S5
PA: 30S ribosomal protein S6
QA: 30S ribosomal protein S7
RA: 30S ribosomal protein S8
SA: 30S ribosomal protein S9
TA: 30S ribosomal protein S10
UA: 30S ribosomal protein S11
VA: 30S ribosomal protein S12
WA: 30S ribosomal protein S13
XA: 30S ribosomal protein S14 type Z
YA: 30S ribosomal protein S15
ZA: 30S ribosomal protein S16
AB: 30S ribosomal protein S17
BB: 30S ribosomal protein S18
CB: 30S ribosomal protein S19
DB: 30S ribosomal protein S20
EB: 30S ribosomal protein Thx
FB: 16S ribosomal RNA
GB: 23S ribosomal RNA
HB: 5S ribosomal RNA
IB: tRNA
JB: 50S ribosomal protein L2
KB: 50S ribosomal protein L3
LB: 50S ribosomal protein L4
MB: 50S ribosomal protein L5
NB: 50S ribosomal protein L6
OB: 50S ribosomal protein L9
PB: 50S ribosomal protein L13
QB: 50S ribosomal protein L14
RB: 50S ribosomal protein L15
SB: 50S ribosomal protein L16
TB: 50S ribosomal protein L17
UB: 50S ribosomal protein L18
VB: 50S ribosomal protein L19
WB: 50S ribosomal protein L20
XB: 50S ribosomal protein L21
YB: 50S ribosomal protein L22
ZB: 50S ribosomal protein L23
AC: 50S ribosomal protein L24
BC: 50S ribosomal protein L25
CC: 50S ribosomal protein L27
DC: 50S ribosomal protein L28
EC: 50S ribosomal protein L29
FC: 50S ribosomal protein L30
GC: 50S ribosomal protein L31
HC: 50S ribosomal protein L32
IC: 50S ribosomal protein L33
JC: 50S ribosomal protein L34
KC: 50S ribosomal protein L35
LC: 50S ribosomal protein L36
MC: mRNA
NC: tRNA
OC: Peptide chain release factor 1
PC: Peptide chain release factor 1
QC: 30S ribosomal protein S2
RC: 30S ribosomal protein S3
SC: 50S ribosomal protein S4
TC: 30S ribosomal protein S5
UC: 30S ribosomal protein S6
VC: 30S ribosomal protein S7
WC: 30S ribosomal protein S8
XC: 30S ribosomal protein S9
YC: 30S ribosomal protein S10
ZC: 30S ribosomal protein S11
AD: 30S ribosomal protein S12
BD: 30S ribosomal protein S13
CD: 30S ribosomal protein S14 type Z
DD: 30S ribosomal protein S15
ED: 30S ribosomal protein S16
FD: 30S ribosomal protein S17
GD: 30S ribosomal protein S18
HD: 30S ribosomal protein S19
ID: 30S ribosomal protein S20
JD: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,622,5541554
Polymers4,586,347114
Non-polymers36,2071440
Water00
1
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: Peptide chain release factor 1
LA: 30S ribosomal protein S2
MA: 30S ribosomal protein S3
NA: 50S ribosomal protein S4
OA: 30S ribosomal protein S5
PA: 30S ribosomal protein S6
QA: 30S ribosomal protein S7
RA: 30S ribosomal protein S8
SA: 30S ribosomal protein S9
TA: 30S ribosomal protein S10
UA: 30S ribosomal protein S11
VA: 30S ribosomal protein S12
WA: 30S ribosomal protein S13
XA: 30S ribosomal protein S14 type Z
YA: 30S ribosomal protein S15
ZA: 30S ribosomal protein S16
AB: 30S ribosomal protein S17
BB: 30S ribosomal protein S18
CB: 30S ribosomal protein S19
DB: 30S ribosomal protein S20
EB: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,311,593790
Polymers2,293,17457
Non-polymers18,419733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
FB: 16S ribosomal RNA
GB: 23S ribosomal RNA
HB: 5S ribosomal RNA
IB: tRNA
JB: 50S ribosomal protein L2
KB: 50S ribosomal protein L3
LB: 50S ribosomal protein L4
MB: 50S ribosomal protein L5
NB: 50S ribosomal protein L6
OB: 50S ribosomal protein L9
PB: 50S ribosomal protein L13
QB: 50S ribosomal protein L14
RB: 50S ribosomal protein L15
SB: 50S ribosomal protein L16
TB: 50S ribosomal protein L17
UB: 50S ribosomal protein L18
VB: 50S ribosomal protein L19
WB: 50S ribosomal protein L20
XB: 50S ribosomal protein L21
YB: 50S ribosomal protein L22
ZB: 50S ribosomal protein L23
AC: 50S ribosomal protein L24
BC: 50S ribosomal protein L25
CC: 50S ribosomal protein L27
DC: 50S ribosomal protein L28
EC: 50S ribosomal protein L29
FC: 50S ribosomal protein L30
GC: 50S ribosomal protein L31
HC: 50S ribosomal protein L32
IC: 50S ribosomal protein L33
JC: 50S ribosomal protein L34
KC: 50S ribosomal protein L35
LC: 50S ribosomal protein L36
MC: mRNA
NC: tRNA
OC: Peptide chain release factor 1
PC: Peptide chain release factor 1
QC: 30S ribosomal protein S2
RC: 30S ribosomal protein S3
SC: 50S ribosomal protein S4
TC: 30S ribosomal protein S5
UC: 30S ribosomal protein S6
VC: 30S ribosomal protein S7
WC: 30S ribosomal protein S8
XC: 30S ribosomal protein S9
YC: 30S ribosomal protein S10
ZC: 30S ribosomal protein S11
AD: 30S ribosomal protein S12
BD: 30S ribosomal protein S13
CD: 30S ribosomal protein S14 type Z
DD: 30S ribosomal protein S15
ED: 30S ribosomal protein S16
FD: 30S ribosomal protein S17
GD: 30S ribosomal protein S18
HD: 30S ribosomal protein S19
ID: 30S ribosomal protein S20
JD: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,310,961764
Polymers2,293,17457
Non-polymers17,787707
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.86, 450.69, 615.88
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 AFBBGBCHBDIAIBNCHAMC

#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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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: 8862.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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50S ribosomal protein ... , 30 types, 60 molecules EJBFKBGLBHMBINBJOBKPBLQBMRBNSBOTBPUBQVBRWBSXB...

#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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I15
#23: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I28
#38: Protein 50S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62664

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Protein , 1 types, 4 molecules JAKAOCPC

#35: Protein
Peptide chain release factor 1 / RF-1


Mass: 41285.090 Da / Num. of mol.: 4 / Mutation: 302-304 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfA / Production host: Escherichia coli (E. coli) / References: UniProt: B7MKB3

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30S ribosomal protein ... , 19 types, 38 molecules LAQCMARCOATCPAUCQAVCRAWCSAXCTAYCUAZCVAADWABDXACDYADDZAEDABFD...

#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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62663
#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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / 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 (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62613

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Non-polymers , 3 types, 1440 molecules

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


Mass: 24.305 Da / Num. of mol.: 1428 / 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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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1861.26
2
3
4
5
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop7.53 uL of 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.
2892vapor diffusion, hanging drop7.53 uL of 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.
2893vapor diffusion, hanging drop7.53 uL of 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.
2894vapor diffusion, hanging drop7.53 uL of 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.
2895vapor diffusion, hanging drop7.53 uL of 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.

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
41004
51005
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 23-ID-D21.033
SYNCHROTRONAPS 23-ID-D31.033
SYNCHROTRONAPS 23-ID-D41.033
SYNCHROTRONAPS 23-ID-D51.033
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELApr 14, 2012
DECTRIS PILATUS3 6M2PIXELApr 14, 2012
DECTRIS PILATUS3 6M3PIXELMar 24, 2012
DECTRIS PILATUS3 6M4PIXELMar 24, 2012
DECTRIS PILATUS3 6M5PIXELMar 24, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
5SINGLE WAVELENGTHMx-ray5
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.0331
31.0331
41.0331
51.0331
ReflectionResolution: 3.4→90 Å / Num. obs: 792709 / % possible obs: 100 % / Redundancy: 38.1 % / Net I/σ(I): 7.75
Reflection shellResolution: 3.4→3.6 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 3.4→50 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs792518 99.9 %
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms95708 201010 1498 0 298216

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