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- PDB-9b1x: HWS19 strain gidB mutant mycobacterial ribosome -

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Basic information

Entry
Database: PDB / ID: 9b1x
TitleHWS19 strain gidB mutant mycobacterial ribosome
Components
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 19
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Conserved domain protein
  • mRNA fragment
KeywordsRIBOSOME / mycobacteria
Function / homology
Function and homology information


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 ...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 / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein 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 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
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Conserved domain protein / Large ribosomal subunit protein bL33A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Conserved domain protein / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsChen, Y. / Young, I.D. / Fraser, J.S. / Javid, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM133129 United States
CitationJournal: To be published
Title: Ribosomal RNA methylation by GidB is a capacitor for discrimination of mischarged tRNA
Authors: Chen, Y. / Young, I.D. / Fraser, J.S. / Javid, B.
History
DepositionMar 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S rRNA
B: Conserved domain protein
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14B
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18B
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
V: Small ribosomal subunit protein uS2
X: mRNA fragment
Y: 23S rRNA
U: 5S rRNA
Z: Large ribosomal subunit protein uL2
a: Large ribosomal subunit protein uL3
b: Large ribosomal subunit protein uL4
c: Large ribosomal subunit protein uL5
d: Large ribosomal subunit protein uL6
e: Large ribosomal subunit protein uL11
f: Large ribosomal subunit protein uL13
g: Large ribosomal subunit protein uL14
h: Large ribosomal subunit protein uL15
i: Large ribosomal subunit protein uL16
j: Large ribosomal subunit protein bL17
k: Large ribosomal subunit protein uL18
l: Large ribosomal subunit protein bL19
m: Large ribosomal subunit protein bL20
n: Large ribosomal subunit protein bL21
o: Large ribosomal subunit protein uL22
p: Large ribosomal subunit protein uL23
q: Large ribosomal subunit protein uL24
r: Large ribosomal subunit protein bL25
s: Large ribosomal subunit protein bL27
t: Large ribosomal subunit protein bL28
u: Large ribosomal subunit protein uL29
5: 50S ribosomal protein bL37
v: Large ribosomal subunit protein uL10
w: Large ribosomal subunit protein uL30
x: Large ribosomal subunit protein bL32
y: Large ribosomal subunit protein bL33A
z: Large ribosomal subunit protein bL34
1: Large ribosomal subunit protein bL35
2: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,273,201683
Polymers2,257,70854
Non-polymers15,493629
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules AXYU

#1: RNA chain 16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: GenBank: 2093960070
#22: RNA chain mRNA fragment


Mass: 1791.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19
#23: RNA chain 23S rRNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: GenBank: 2198294598
#24: RNA chain 5S rRNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: GenBank: 967054

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide Conserved domain protein


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QR10

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Small ribosomal subunit protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPQRSTV

#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD7
#4: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSL7
#5: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG6
#6: Protein Small ribosomal subunit protein bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0A2U9Q0X2
#7: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QS97
#8: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG3
#9: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSP9
#10: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD0
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSL6
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QS96
#13: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSL5
#14: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG2
#15: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QVQ3
#16: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QV37
#17: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSE0
#18: Protein Small ribosomal subunit protein bS18B / 30S ribosomal protein S18 2


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R7F7
#19: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD5
#20: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R102
#21: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QVB8

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Large ribosomal subunit protein ... , 28 types, 28 molecules Zabcdefghijklmnopqrstuvwxyz1

#25: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD4
#26: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD1
#27: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD2
#28: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG1
#29: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG4
#30: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QS45
#31: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSP8
#32: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSF9
#33: Protein Large ribosomal subunit protein uL15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG8
#34: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD8
#35: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSL9
#36: Protein Large ribosomal subunit protein uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG5
#37: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QV42
#38: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QYU6
#39: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R151
#40: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD6
#41: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD3
#42: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG0
#43: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R3D2
#44: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R150
#45: Protein Large ribosomal subunit protein bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QV03
#46: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSD9
#48: Protein Large ribosomal subunit protein uL10 / 50S ribosomal protein L10


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QS62
#49: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSG7
#50: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R3I9
#51: Protein Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QS39
#52: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0R7K0
#53: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QYU7

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50S ribosomal protein ... , 2 types, 2 molecules 52

#47: Protein/peptide 50S ribosomal protein bL37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QTP4
#54: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: HWS19 / References: UniProt: A0QSL4

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Non-polymers , 2 types, 629 molecules

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


Mass: 24.305 Da / Num. of mol.: 624 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium smegmatis ribosome, HWS19 strain, gidB mutant
Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: HWS19
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA positive charge / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.2 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 150 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.991 sec. / Electron dose: 72.704 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5831

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Processing

EM software
IDNameVersionCategory
1cisTEMdevelopmentparticle selection
2SerialEMimage acquisition
3cisTEMdevelopmentCTF correction
4UCSF ChimeraXmodel fitting
5ISOLDEmodel fitting
6Cootmodel fitting
7PyMOLmodel fitting
12cisTEMdevelopmentinitial Euler assignment
13cisTEMdevelopmentfinal Euler assignment
14cisTEMdevelopmentclassification
15cisTEMdevelopment3D reconstruction
16PHENIX1.19.2_4158:model refinement
17ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136418 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15o60

5o60

15o601PDBexperimental model
25o5j

5o5j

15o5jPDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002156589
ELECTRON MICROSCOPYf_angle_d0.481234229
ELECTRON MICROSCOPYf_dihedral_angle_d14.92961477
ELECTRON MICROSCOPYf_chiral_restr0.03529955
ELECTRON MICROSCOPYf_plane_restr0.00412676

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